Rationally designed, synthetic antibody libraries and uses therefor

ABSTRACT

The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity. The libraries are designed to reflect the preimmune repertoire naturally created by the human immune system and are based on rational design informed by examination of publicly available databases of human antibody sequences.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of application Ser. No. 12/210,072,filed Sep. 12, 2008, which claims the benefit of U.S. ProvisionalApplication No. 60/993,785, filed on Sep. 14, 2007; the contents ofthese applications are hereby incorporated by reference in theirentirety.

SEQUENCE LISTING

In accordance with 37 CFR §1.52(e)(5), the present specification makesreference to a Sequence Listing (submitted electronically as a .txt filenamed “SeqList1.txt” on Jan. 8, 2014). The .txt file was generated onJan. 8, 2014 and is 220 kb in size. The entire contents of the SequenceListing are herein incorporated by reference.

BACKGROUND OF THE INVENTION

Antibodies have profound relevance as research tools and in diagnosticand therapeutic applications. However, the identification of usefulantibodies is difficult and once identified, antibodies often requireconsiderable redesign or ‘humanization’ before they are suitable fortherapeutic applications.

Previous methods for identifying desirable antibodies have typicallyinvolved phage display of representative antibodies, for example humanlibraries derived by amplification of nucleic acids from B cells ortissues, or, alternatively, synthetic libraries. However, theseapproaches have limitations. For example, most human libraries known inthe art contain only the antibody sequence diversity that can beexperimentally captured or cloned from the source (e.g., B cells).Accordingly, the human library may completely lack or under-representcertain useful antibody sequences. Synthetic or consensus librariesknown in the art have other limitations, such as the potential to encodenon-naturally occurring (e.g., non-human) sequences that have thepotential to be immunogenic. Moreover, certain synthetic libraries ofthe art suffer from at least one of two limitations: (1) the number ofmembers that the library can theoretically contain (i.e., theoreticaldiversity) may be greater than the number of members that can actuallybe synthesized, and (2) the number of members actually synthesized maybe so great as to preclude screening of each member in a physicalrealization of the library, thereby decreasing the probability that alibrary member with a particular property may be isolated.

For example, a physical realization of a library (e.g., yeast display,phage display, ribosomal display, etc.) capable of screening 10¹²library members will only sample about 10% of the sequences contained ina library with 10¹³ members. Given a median CDRH3 length of about 12.7amino acids (Rock et al., J. Exp. Med., 1994, 179:323-328), the numberof theoretical sequence variants in CDRH3 alone is about 20^(12.7), orabout 3.3×10¹⁶ variants. This number does not account for knownvariation that occurs in CDRH1 and CDRH2, heavy chain framework regions,and pairing with different light chains, each of which also exhibitvariation in their respective CDRL1, CDRL2, and CDRL3. Finally, theantibodies isolated from these libraries are often not amenable torational affinity maturation techniques to improve the binding of thecandidate molecule.

Accordingly, a need exists for smaller (i.e., able to be synthesized andphysically realizable) antibody libraries with directed diversity thatsystematically represent candidate antibodies that are non-immunogenic(i.e., more human) and have desired properties (e.g., the ability torecognize a broad variety of antigens). However, obtaining suchlibraries requires balancing the competing objectives of restricting thesequence diversity represented in the library (to enable synthesis andphysical realization, potentially with oversampling, while limiting theintroduction of non-human sequences) while maintaining a level ofdiversity sufficient to recognize a broad variety of antigens. Prior tothe instant invention, it was known in the art that “[al]thoughlibraries containing heavy chain CDR3 length diversity have beenreported, it is impossible to synthesize DNA encoding both the sequenceand the length diversity found in natural heavy chain CDR3 repertoires”(Hoet et al., Nat. Biotechnol., 2005, 23: 344, incorporated by referencein its entirety).

Therefore, it would be desirable to have antibody libraries which (a)can be readily synthesized, (b) can be physically realized and, incertain cases, oversampled, (c) contain sufficient diversity torecognize all antigens recognized by the preimmune human repertoire(i.e., before negative selection), (d) are non-immunogenic in humans(i.e., comprise sequences of human origin), and (e) contain CDR lengthand sequence diversity, and framework diversity, representative ofnaturally-occurring human antibodies. Embodiments of the instantinvention at least provide, for the first time, antibody libraries thathave these desirable features.

SUMMARY OF THE INVENTION

The present invention is relates to, at least, synthetic polynucleotidelibraries, methods of producing and using the libraries of theinvention, kits and computer readable forms including the libraries ofthe invention. In some embodiments, the libraries of the invention aredesigned to reflect the preimmune repertoire naturally created by thehuman immune system and are based on rational design informed byexamination of publicly available databases of human antibody sequences.It will be appreciated that certain non-limiting embodiments of theinvention are described below. As described throughout thespecification, the invention encompasses many other embodiments as well.

In certain embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode at least 10⁶ uniqueantibody CDRH3 amino acid sequences comprising:

-   -   (i) an N1 amino acid sequence of 0 to about 3 amino acids,        wherein each amino acid of the N1 amino acid sequence is among        the 12 most frequently occurring amino acids at the        corresponding position in N1 amino acid sequences of CDRH3 amino        acid sequences that are functionally expressed by human B cells;    -   (ii) a human CDRH3 DH amino acid sequence, N- and C-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them;    -   (iii) an N2 amino acid sequence of 0 to about 3 amino acids,        wherein each amino acid of the N2 amino acid sequence is among        the 12 most frequently occurring amino acids at the        corresponding position in N2 amino acid sequences of CDRH3 amino        acid sequences that are functionally expressed by human B cells;        and    -   (iv) a human CDRH3 H3-JH amino acid sequence, N-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them.

In other embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode at least about 10⁶unique antibody CDRH3 amino acid sequences comprising:

-   -   (i) an N1 amino acid sequence of 0 to about 3 amino acids,        wherein:        -   (a) the most N-terminal N1 amino acid, if present, is            selected from a group consisting of R, G, P, L, S, A, V, K,            I, Q, T and D;        -   (b) the second most N-terminal N1 amino acid, if present, is            selected from a group consisting of G, P, R, S, L, V, E, A,            D, I, T and K; and        -   (c) the third most N-terminal N1 amino acid, if present, is            selected from the group consisting of G, R, P, S, L, A, V,            T, E, D, K and F;    -   (ii) a human CDRH3 DH amino acid sequence, N- and C-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them;    -   (iii) an N2 amino acid sequence of 0 to about 3 amino acids,        wherein:        -   (a) the most N-terminal N2 amino acid, if present, is            selected from a group consisting of G, P, R, L, S, A, T, V,            E, D, F and H;        -   (b) the second most N-terminal N2 amino acid, if present, is            selected from a group consisting of G, P, R, S, T, L, A, V,            E, Y, D and K; and        -   (c) the third most N-terminal N2 amino acid, if present, is            selected from the group consisting of G, P, S, R, L, A, T,            V, D, E, W and Q; and    -   (iv) a human CDRH3 H3-JH amino acid sequence, N-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them.

In still other embodiments, the invention comprises a library ofsynthetic polynucleotides, wherein said polynucleotides encode at leastabout 10⁶ unique antibody CDRH3 amino acid sequences that are at leastabout 80% identical to an amino acid sequence represented by thefollowing formula:

[X]-[N1]-[DH]-[N2]-[H3-JH], wherein:

-   -   (i) X is any amino acid residue or no amino acid residue;    -   (ii) N1 is an amino acid sequence selected from the group        consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL,        GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV,        RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG,        PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT,        GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA,        EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL,        QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK,        SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE,        AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL,        SGL, SSE, TGL, WGT, and combinations thereof;    -   (iii) DH is an amino acid sequence selected from the group        consisting of all possible reading frames that do not include a        stop codon encoded by IGHD1-1 (SEQ ID NO: 501), IGHD1-20 (SEQ ID        NO: 503), IGHD1-26 (polynucleotides encoding SEQ ID NOs: 13 and        14), IGHD1-7 (SEQ ID NO: 504), IGHD2-15 (polynucleotides        encoding SEQ ID NO: 16), IGHD2-2 (polynucleotides encoding SEQ        ID NOs: 10 and 11), IGHD2-21 (SEQ ID NOs: 505 and 506), IGHD2-8        (SEQ ID NO: 507), IGHD3-10 (polynucleotides encoding SEQ ID NOs:        1-3), IGHD3-16 (SEQ ID NO: 508), IGHD3-22 (polynucleotides        encoding SEQ ID NO: 4), IGHD3-3 (polynucleotides encoding SEQ ID        NO: 9), IGHD3-9 (SEQ ID NO: 509), IGHD4-17 (polynucleotides        encoding SEQ ID NO: 12), IGHD4-23 (SEQ ID NO: 510), IGHD4-4 (SEQ        ID NO: 511), IGHD-4-11 (SEQ ID NO: 511), IGHD5-12 (SEQ ID NO:        512), IGHD5-24 (SEQ ID NO: 513), IGHD5-5 (polynucleotides        encoding SEQ ID NO: 15), IGHD-5-18 (polynucleotides encoding SEQ        ID NO: 15), IGHD6-13 (polynucleotides encoding SEQ ID NOs: 7 and        8), IGHD6-19 (polynucleotides encoding SEQ ID NOs: 5 and 6),        IGHD6-25 (SEQ ID NO: 514), IGHD6-6 (SEQ ID NO: 515), and        IGHD7-27 (SEQ ID NO: 516), and N- and C-terminal truncations        thereof;    -   (iv) N2 is an amino acid sequence selected from the group        consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL,        GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV,        RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG,        PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT,        GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA,        EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL,        QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK,        SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE,        AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL,        SGL, SSE, TGL, WGT, and combinations thereof; and    -   (v) H3-JH is an amino acid sequence selected from the group        consisting of AEYFQH (SEQ ID NO: 17), EYFQH (SEQ ID NO: 583),        YFQH (SEQ ID NO: 584), FQH, QH, H, YWYFDL (SEQ ID NO: 18), WYFDL        (SEQ ID NO: 585), YFDL (SEQ ID NO: 586), FDL, DL, L, AFDV (SEQ        ID NO: 19), FDV, DV, V, YFDY (SEQ ID NO: 20), FDY, DY, Y, NWFDS        (SEQ ID NO: 21), WFDS (SEQ ID NO: 587), FDS, DS, S, YYYYYGMDV        (SEQ ID NO: 22), YYYYGMDV (SEQ ID NO: 588), YYYGMDV (SEQ ID NO:        589), YYGMDV (SEQ ID NO: 590), YGMDV (SEQ ID NO: 591), GMDV (SEQ        ID NO: 592), and MDV, or a sequence of at least 80% identity to        any of them.

In still another embodiment, the invention comprises wherein saidlibrary consists essentially of a plurality of polynucleotides encodingCDRH3 amino acid sequences that are at least about 80% identical to anamino acid sequence represented by the following formula:

[X]-[N1]-[DH]-[N2]-[H3-JH], wherein:

-   -   (i) X is any amino acid residue or no amino acid residue;    -   (ii) N1 is an amino acid sequence selected from the group        consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL,        GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV,        RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG,        PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT,        GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA,        EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL,        QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK,        SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE,        AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL,        SGL, SSE, TGL, WGT, and combinations thereof;    -   (iii) DH is an amino acid sequence selected from the group        consisting of all possible reading frames that do not include a        stop codon encoded by IGHD1-1 (SEQ ID NO: 501), IGHD1-20 (SEQ ID        NO: 503), IGHD1-26 (polynucleotides encoding SEQ ID NOs: 13 and        14), IGHD1-7 (SEQ ID NO: 504), IGHD2-15 (polynucleotides        encoding SEQ ID NO: 16), IGHD2-2 (polynucleotides encoding SEQ        ID NOs: 10 and 11), IGHD2-21 (SEQ ID NOs: 505 and 506), IGHD2-8        (SEQ ID NO: 507), IGHD3-10 (polynucleotides encoding SEQ ID NOs:        1-3), IGHD3-16 (SEQ ID NO: 508), IGHD3-22 (polynucleotides        encoding SEQ ID NO: 4), IGHD3-3 (polynucleotides encoding SEQ ID        NO: 9), IGHD3-9 (SEQ ID NO: 509), IGHD4-17 (polynucleotides        encoding SEQ ID NO: 12), IGHD4-23 (SEQ ID NO: 510), IGHD4-4 (SEQ        ID NO: 511), IGHD-4-11 (SEQ ID NO: 511), IGHD5-12 (SEQ ID NO:        512), IGHD5-24 (SEQ ID NO: 513), IGHD5-5 (polynucleotides        encoding SEQ ID NO: 15), IGHD-5-18 (polynucleotides encoding SEQ        ID NO: 15), IGHD6-13 (polynucleotides encoding SEQ ID NOs: 7 and        8), IGHD6-19 (polynucleotides encoding SEQ ID NOs: 5 and 6),        IGHD6-25 (SEQ ID NO: 514), IGHD6-6 (SEQ ID NO: 515), and        IGHD7-27 (SEQ ID NO: 516), and N- and C-terminal truncations        thereof;    -   (iv) N2 is an amino acid sequence selected from the group        consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL,        GT, GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV,        RP, AP, SP, LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG,        PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT,        GGV, D, E, F, H, I, K, M, Q, W, Y, AR, AS, AT, AY, DL, DT, EA,        EK, FH, FS, HL, HW, IS, KV, LD, LE, LR, LS, LT, NR, NT, QE, QL,        QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA, SD, SE, SF, SI, SK,        SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS, WS, YS, AAE,        AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA, SAL,        SGL, SSE, TGL, WGT, and combinations thereof; and    -   (v) H3-JH is an amino acid sequence selected from the group        consisting of AEYFQH (SEQ ID NO: 17), EYFQH (SEQ ID NO: 583),        YFQH (SEQ ID NO: 584), FQH, QH, H, YWYFDL (SEQ ID NO: 18), WYFDL        (SEQ ID NO: 585), YFDL (SEQ ID NO: 586), FDL, DL, L, AFDV (SEQ        ID NO: 19), FDV, DV, V, YFDY (SEQ ID NO: 20), FDY, DY, Y, NWFDS        (SEQ ID NO: 21), WFDS (SEQ ID NO: 587), FDS, DS, S, YYYYYGMDV        (SEQ ID NO: 22), YYYYGMDV (SEQ ID NO: 588), YYYGMDV (SEQ ID NO:        589), YYGMDV (SEQ ID NO: 590), YGMDV (SEQ ID NO: 591), GMDV (SEQ        ID NO: 592), and MDV, or a sequence of at least 80% identity to        any of them.

In another embodiment, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode one or more fulllength antibody heavy chain sequences, and wherein the CDRH3 amino acidsequences of the heavy chain comprise:

-   -   (i) an N1 amino acid sequence of 0 to about 3 amino acids,        wherein each amino acid of the N1 amino acid sequence is among        the 12 most frequently occurring amino acids at the        corresponding position in N1 amino acid sequences of CDRH3 amino        acid sequences that are functionally expressed by human B cells;    -   (ii) a human CDRH3 DH amino acid sequence, N- and C-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them;    -   (iii) an N2 amino acid sequence of 0 to about 3 amino acids,        wherein each amino acid of the N2 amino acid sequence is among        the 12 most frequently occurring amino acids at the        corresponding position in N2 amino acid sequences of CDRH3 amino        acid sequences that are functionally expressed by human B cells;        and    -   (iv) a human CDRH3 H3-JH amino acid sequence, N-terminal        truncations thereof, or a sequence of at least about 80%        identity to any of them.

The following embodiments may be applied throughout the embodiments ofthe instant invention. In one aspect, one or more CDRH3 amino acidsequences further comprise an N-terminal tail residue. In still anotheraspect, the N-terminal tail residue is selected from the groupconsisting of G, D, and E.

In yet another aspect, the N1 amino acid sequence is selected from thegroup consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL, GT,GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV, RP, AP, SP,LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG, PGG, RGG, AGG, SGG,LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT, GGV, D, E, F, H, I, K, M,Q, W, Y, AR, AS, AT, AY, DL, DT, EA, EK, FH, FS, HL, HW, IS, KV, LD, LE,LR, LS, LT, NR, NT, QE, QL, QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA,SD, SE, SF, SI, SK, SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS,WS, YS, AAE, AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA,SAL, SGL, SSE, TGL, WGT, and combinations thereof. In certain otheraspects, the N1 amino acid sequence may be of about 0 to about 5 aminoacids.

In yet another aspect, the N2 amino acid sequence is selected from thegroup consisting of G, P, R, A, S, L, T, V, GG, GP, GR, GA, GS, GL, GT,GV, PG, RG, AG, SG, LG, TG, VG, PP, PR, PA, PS, PL, PT, PV, RP, AP, SP,LP, TP, VP, GGG, GPG, GRG, GAG, GSG, GLG, GTG, GVG, PGG, RGG, AGG, SGG,LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL, GGT, GGV, D, E, F, H, I, K, M,Q, W, Y, AR, AS, AT, AY, DL, DT, EA, EK, FH, FS, HL, HW, IS, KV, LD, LE,LR, LS, LT, NR, NT, QE, QL, QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA,SD, SE, SF, SI, SK, SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS,WS, YS, AAE, AYH, DTL, EKR, ISR, NTP, PKS, PRP, PTA, PTQ, REL, RPL, SAA,SAL, SGL, SSE, TGL, WGT, and combinations thereof. In certain otheraspects, the N2 sequence may be of about 0 to about 5 amino acids.

In yet another aspect, the H3-JH amino acid sequence is selected fromthe group consisting of AEYFQH (SEQ ID NO: 17), EYFQH (SEQ ID NO: 583),YFQH (SEQ ID NO: 584), FQH, QH, H, YWYFDL (SEQ ID NO: 18), WYFDL (SEQ IDNO: 585), YFDL (SEQ ID NO: 586), FDL, DL, L, AFDV (SEQ ID NO: 19), FDV,DV, V, YFDY (SEQ ID NO: 20), FDY, DY, Y, NWFDS (SEQ ID NO: 21), WFDS(SEQ ID NO: 587), FDS, DS, S, YYYYYGMDV (SEQ ID NO: 22), YYYYGMDV (SEQID NO: 588), YYYGMDV (SEQ ID NO: 589), YYGMDV (SEQ ID NO: 590), YGMDV(SEQ ID NO: 591), GMDV (SEQ ID NO: 592), and MDV.

In other embodiments, the invention comprises a library of syntheticpolynucleotides encoding a plurality of antibody CDRH3 amino acidsequences, wherein the percent occurrence within the central loop of theCDRH3 amino acid sequences of at least one of the following i-i+1 pairsin the library is within the ranges specified below:

-   -   Tyr-Tyr in an amount from about 2.5% to about 6.5%;    -   Ser-Gly in an amount from about 2.5% to about 4.5%;    -   Ser-Ser in an amount from about 2% to about 4%;    -   Gly-Ser in an amount from about 1.5% to about 4%;    -   Tyr-Ser in an amount from about 0.75% to about 2%;    -   Tyr-Gly in an amount from about 0.75% to about 2%; and    -   Ser-Tyr in an amount from about 0.75% to about 2%.

In still other embodiments, the invention comprises a library ofsynthetic polynucleotides encoding a plurality of antibody CDRH3 aminoacid sequences, wherein the percent occurrence within the central loopof the CDRH3 amino acid sequences of at least one of the following i-i+2pairs in the library is within the ranges specified below:

-   -   Tyr-Tyr in an amount from about 2.5% to about 4.5%;    -   Gly-Tyr in an amount from about 2.5% to about 5.5%;    -   Ser-Tyr in an amount from about 2% to about 4%;    -   Tyr-Ser in an amount from about 1.75% to about 3.75%;    -   Ser-Gly in an amount from about 2% to about 3.5%;    -   Ser-Ser in an amount from about 1.5% to about 3%;    -   Gly-Ser in an amount from about 1.5% to about 3%; and    -   Tyr-Gly in an amount from about 1% to about 2%.

In another embodiment, the invention comprises a library of syntheticpolynucleotides encoding a plurality of antibody CDRH3 amino acidsequences, wherein the percent occurrence within the central loop of theCDRH3 amino acid sequences of at least one of the following i-i+3 pairsin the library is within the ranges specified below:

-   -   Gly-Tyr in an amount from about 2.5% to about 6.5%;    -   Ser-Tyr in an amount from about 1% to about 5%;    -   Tyr-Ser in an amount from about 2% to about 4%;    -   Ser-Ser in an amount from about 1% to about 3%;    -   Gly-Ser in an amount from about 2% to about 5%; and    -   Tyr-Tyr in an amount from about 0.75% to about 2%.

In one aspect of the invention, at least 2, 3, 4, 5, 6, or 7 of thespecified i-i+1 pairs in the library are within the specified ranges. Inanother aspect, the CDRH3 amino acid sequences are human. In yet anotheraspect, the polynucleotides encode at least about 10⁶ unique CDRH3 aminoacid sequences.

In other aspects of the invention, the polynucleotides further encodeone or more heavy chain chassis amino acid sequences that are N-terminalto the CDRH3 amino acid sequences, and the one or more heavy chainchassis sequences are selected from the group consisting of about Kabatamino acid 1 to about Kabat amino acid 94 encoded by IGHV1-2 (SEQ ID NO:24), IGHV1-3 (SEQ ID NO: 423), IGHV1-8 (SEQ ID NOs: 424, 425), IGHV1-18(SEQ ID NO: 25), IGHV1-24 (SEQ ID NO: 426), IGHV1-45 (SEQ ID NO: 427),IGHV1-46 (SEQ ID NO: 26), IGHV1-58 (SEQ ID NO: 428), IGHV1-69 (SEQ IDNO: 27), IGHV2-5 (SEQ ID NO: 429), IGHV2-26 (SEQ ID NO: 430), IGHV2-70(SEQ ID NO: 431, 432), IGHV3-7 (SEQ ID NO: 28), IGHV3-9 (SEQ ID NO:433), IGHV3-11 (SEQ ID NO: 434), IGHV3-13 (SEQ ID NO: 435), IGHV3-15(SEQ ID NO: 29), IGHV3-20 (SEQ ID NO: 436), IGHV3-21 (SEQ ID NO: 437),IGHV3-23 (SEQ ID NO: 30), IGHV3-30 (SEQ ID NO: 31), IGHV3-33 (SEQ ID NO:32), IGHV3-43 (SEQ ID NO: 438), IGHV3-48 (SEQ ID NO: 33), IGHV3-49 (SEQID NO: 439), IGHV3-53 (SEQ ID NO: 440), IGHV3-64 (SEQ ID NO: 441),IGHV3-66 (SEQ ID NO: 442), IGHV3-72 (SEQ ID NO: 443), IGHV3-73 (SEQ IDNO: 444), IGHV3-74 (SEQ ID NO: 445), IGHV4-4 (SEQ ID NO: 446, 447),IGHV4-28 (SEQ ID NO: 448), IGHV4-31 (SEQ ID NO: 34), IGHV4-34 (SEQ IDNO: 35), IGHV4-39 (SEQ ID NO: 36), IGHV4-59 (SEQ ID NO: 37), IGHV4-61(SEQ ID NO: 38), IGHV4-B (SEQ ID NO: 39), IGHV5-51 (SEQ ID NO: 40),IGHV6-1 (SEQ ID NO: 449), and IGHV7-4-1 (SEQ ID NO: 450), or a sequenceof at least about 80% identity to any of them.

In another aspect, the polynucleotides further encode one or more FRM4amino acid sequences that are C-terminal to the CDRH3 amino acidsequences, wherein the one or more FRM4 amino acid sequences areselected from the group consisting of a FRM4 amino acid sequence encodedby IGHJ1 (SEQ ID NO: 253), IGHJ2 (SEQ ID NO: 254), IGHJ3 (SEQ ID NO:255), IGHJ4 (SEQ ID NO: 256), IGHJ5 (SEQ ID NO: 257), and IGHJ6 (SEQ IDNO: 257), or a sequence of at least about 80% identity to any of them.In still another aspect, the polynucleotides further encode one or moreimmunoglobulin heavy chain constant region amino acid sequences that areC-terminal to the FRM4 sequence.

In yet another aspect, the CDRH3 amino acid sequences are expressed aspart of full-length heavy chains. In other aspects, the full-lengthheavy chains are selected from the group consisting of an IgG1, IgG2,IgG3, and IgG4, or combinations thereof. In one embodiment, the CDRH3amino acid sequences are from about 2 to about 30, from about 8 to about19, or from about 10 to about 18 amino acid residues in length. In otheraspects, the synthetic polynucleotides of the library encode from about10⁶ to about 10¹⁴, from about 10⁷ to about 10¹³, from about 10⁸ to about10¹², from about 10⁹ to about 10¹², or from about 10¹⁰ to about 10¹²unique CDRH3 amino acid sequences.

In certain embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofantibody VKCDR3 amino acid sequences comprising about 1 to about 10 ofthe amino acids found at Kabat positions 89, 90, 91, 92, 93, 94, 95,95A, 96, and 97, in selected VKCDR3 amino acid sequences derived from aparticular IGKV or IGKJ germline sequence.

In one aspect, the synthetic polynucleotides encode one or more of theamino acid sequences listed in Table 33 or a sequence at least about 80%identical to any of them.

In some embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofunique antibody VKCDR3 amino acid sequences that are of at least about80% identity to an amino acid sequence represented by the followingformula:

[VK_Chassis]-[L3-VK]-[X]-[JK*], wherein:

-   -   (i) VK_Chassis is an amino acid sequence selected from the group        consisting of about Kabat amino acid 1 to about Kabat amino acid        88 encoded by IGKV1-05 (SEQ ID NO: 229), IGKV1-06 (SEQ ID NO:        451), IGKV1-08 (SEQ ID NO: 452, 453), IGKV1-09 (SEQ ID NO: 454),        IGKV1-12 (SEQ ID NO: 230), IGKV1-13 (SEQ ID NO: 455), IGKV1-16        (SEQ ID NO: 456), IGKV1-17 (SEQ ID NO: 457), IGKV1-27 (SEQ ID        NO: 231), IGKV1-33 (SEQ ID NO: 232), IGKV1-37 (SEQ ID NOs: 458,        459), IGKV1-39 (SEQ ID NO: 233), IGKV1D-16 (SEQ ID NO: 460),        IGKV1D-17 (SEQ ID NO: 461), IGKV1D-43 (SEQ ID NO: 462), IGKV1D-8        (SEQ ID NOs: 463, 464), IGKV1-24 (SEQ ID NO: 465), IGKV1-28 (SEQ        ID NO: 234), IGKV1-29 (SEQ ID NO: 466), IGKV1-30 (SEQ ID NO:        467), IGKV1-40 (SEQ ID NO: 468), IGKV1D-26 (SEQ ID NO: 469),        IGKV1D-29 (SEQ ID NO: 470), IGKV1D-30 (SEQ ID NO: 471), IGKV3-11        (SEQ ID NO: 235), IGKV3-15 (SEQ ID NO: 236), IGKV3-20 (SEQ ID        NO: 237), IGKV3D-07 (SEQ ID NO: 472), IGKV3D-11 (SEQ ID NO:        473), IGKV3D-20 (SEQ ID NO: 474), IGKV4-1 (SEQ ID NO: 238),        IGKV5-2 (SEQ ID NOs: 475, 476), IGKV6-21 (SEQ ID NOs: 477), and        IGKV6D-41, or a sequence of at least about 80% identity to any        of them;    -   (ii) L3-VK is the portion of the VKCDR3 encoded by the IGKV gene        segment; and    -   (iii) X is any amino acid residue; and    -   (iv) JK* is an amino acid sequence selected from the group        consisting of sequences encoded by IGJK1, IGJK2, IGJK3, IGJK4,        and IGJK5, wherein the first residue of each IGJK sequence is        not present.

In still other aspects, X may be selected from the group consisting ofF, L, I, R, W, Y, and P.

In certain embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofVλCDR3 amino acid sequences that are of at least about 80% identity toan amino acid sequence represented by the following formula:

[Vλ_Chassis]-[L3-Vλ]-[Jλ], wherein:

-   -   (i) Vλ_Chassis is an amino acid sequence selected from the group        consisting of about Kabat amino acid 1 to about Kabat amino acid        88 encoded by IGλV1-36 (SEQ ID NO: 480), IGλV1-40 (SEQ ID NO:        531), IGλV1-44 (SEQ ID NO: 532), IGλV1-47 (SEQ ID NO: 481),        IGλV1-51 (SEQ ID NO: 533), IGλV10-54 (SEQ ID NO: 482), IGλV1-11        (SEQ ID NOS: 483, 484), IGλV1-14 (SEQ ID NO: 534), IGλV1-18 (SEQ        ID NO: 485), IGλV1-23 (SEQ ID NOS: 486, 487), IGλV1-8 (SEQ ID        NO: 488), IGλV3-1 (SEQ ID NO: 535), IGλV3-10 (SEQ ID NO: 489),        IGλV3-12 (SEQ ID NO: 490), IGλV3-16 (SEQ ID NO: 491), IGλV3-19        (SEQ ID NO: 536), IGλV3-21 (SEQ ID NO: 537), IGλV3-25 (SEQ ID        NO: 492), IGλV3-27 (SEQ ID NO: 493), IGλV3-9 (SEQ ID NO: 494),        IGλV4-3 (SEQ ID NO: 495), IGλV4-60 (SEQ ID NO: 496), IGλV4-69        (SEQ ID NO: 538), IGλV5-39 (SEQ ID NO: 497), IGλV5-45 (SEQ ID        NO: 540), IGλV6-57 (SEQ ID NO: 539), IGλV7-43 (SEQ ID NO: 541),        IGλV7-46 (SEQ ID NO: 498), IGλV8-61 (SEQ ID NO: 499), IGλV9-49        (SEQ ID NO: 500), and IGλV10-54 (SEQ ID NO: 482), or a sequence        of at least about 80% identity to any of them;    -   (ii) L3-Vλ is the portion of the VλCDR3 encoded by the IGλV        segment; and    -   (iii) Jλ is an amino acid sequence selected from the group        consisting of sequences encoded by IGλJ1-01, IGλJ2-01, IGλJ3-01,        IGλJ3-02, IGλJ6-01, IGλJ7-01, and IGλJ7-02, and wherein the        first residue of each IGJλ sequence may or may not be deleted.

In further aspects, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofantibody proteins comprising:

-   -   (i) a CDRH3 amino acid sequence of claim 1; and    -   (ii) a VKCDR3 amino acid sequence comprising about 1 to about 10        of the amino acids found at Kabat positions 89, 90, 91, 92, 93,        94, 95, 95A, 96, and 97, in selected VKCDR3 sequences derived        from a particular IGKV or IGKJ germline sequence.

In still further aspects, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofantibody proteins comprising:

-   -   (i) a CDRH3 amino acid sequence of claim 1; and    -   (ii) a VKCDR3 amino acid sequences of at least about 80%        identity to an amino acid sequence represented by the following        formula:

[VK_Chassis]-[L3-VK]-[X]-[JK*], wherein:

-   -   (a) VK_Chassis is an amino acid sequence selected from the group        consisting of about Kabat amino acid 1 to about Kabat amino acid        88 encoded by IGKV1-05 (SEQ ID NO: 229), IGKV1-06 (SEQ ID NO:        451), IGKV1-08 (SEQ ID NO: 452, 453), IGKV1-09 (SEQ ID NO: 454),        IGKV1-12 (SEQ ID NO: 230), IGKV1-13 (SEQ ID NO: 455), IGKV1-16        (SEQ ID NO: 456), IGKV1-17 (SEQ ID NO: 457), IGKV1-27 (SEQ ID        NO: 231), IGKV1-33 (SEQ ID NO: 232), IGKV1-37 (SEQ ID NOs: 458,        459), IGKV1-39 (SEQ ID NO: 233), IGKV1D-16 (SEQ ID NO: 460),        IGKV1D-17 (SEQ ID NO: 461), IGKV1D-43 (SEQ ID NO: 462), IGKV1D-8        (SEQ ID NOs: 463, 464), IGKV2-24 (SEQ ID NO: 465), IGKV2-28 (SEQ        ID NO: 234), IGKV2-29 (SEQ ID NO: 466), IGKV2-30 (SEQ ID NO:        467), IGKV2-40 (SEQ ID NO: 468), IGKV2D-26 (SEQ ID NO: 469),        IGKV2D-29 (SEQ ID NO: 470), IGKV2D-30 (SEQ ID NO: 471), IGKV3-11        (SEQ ID NO: 235), IGKV3-15 (SEQ ID NO: 236), IGKV3-20, IGKV3D-07        (SEQ ID NO: 472), IGKV3D-11 (SEQ ID NO: 473), IGKV3D-20 (SEQ ID        NO: 474), IGKV4-1 (SEQ ID NO: 238), IGKV5-2 (SEQ ID NOs: 475,        476), IGKV6-21 (SEQ ID NOs: 477), and IGKV6D-41, or a sequence        of at least about 80% identity to any of them;    -   (b) L3-VK is the portion of the VKCDR3 encoded by the IGKV gene        segment; and    -   (c) X is any amino acid residue; and    -   (d) JK* is an amino acid sequence selected from the group        consisting of sequences encoded by IGJK1, IGJK2, IGJK3, IGJK4,        and IGJK5, wherein the first residue of each IGJK sequence is        not present.

In some aspects, the VKCDR3 amino acid sequence comprises one or more ofthe sequences listed in Table 33 or a sequence at least about 80%identical to any of them. In other aspects, the antibody proteins areexpressed in a heterodimeric form. In yet another aspect, the humanantibody proteins are expressed as antibody fragments. In still otheraspects of the invention, the antibody fragments are selected from thegroup consisting of Fab, Fab′, F(ab′)₂, Fv fragments, diabodies, linearantibodies, and single-chain antibodies.

In certain embodiments, the invention comprises an antibody isolatedfrom the polypeptide expression products of any library describedherein.

In still other aspects, the polynucleotides further comprise a 5′polynucleotide sequence and a 3′ polynucleotide sequence that facilitatehomologous recombination.

In one embodiment, the polynucleotides further encode an alternativescaffold.

In another embodiment, the invention comprises a library of polypeptidesencoded by any of the synthetic polynucleotide libraries describedherein.

In yet another embodiment, the invention comprises a library of vectorscomprising any of the polynucleotide libraries described herein. Incertain other aspects, the invention comprises a population of cellscomprising the vectors of the instant invention.

In one aspect, the doubling time of the population of cells is fromabout 1 to about 3 hours, from about 3 to about 8 hours, from about 8 toabout 16 hours, from about 16 to about 20 hours, or from 20 to about 30hours. In yet another aspect, the cells are yeast cells. In stillanother aspect, the yeast is Saccharomyces cerevisiae.

In other embodiments, the invention comprises a library that has atheoretical total diversity of N unique CDRH3 sequences, wherein N isabout 10⁶ to about 10¹⁵; and wherein the physical realization of thetheoretical total CDRH3 diversity has a size of at least about 3N,thereby providing a probability of at least about 95% that anyindividual CDRH3 sequence contained within the theoretical totaldiversity of the library is present in the actual library.

In certain embodiments, the invention comprises a library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofantibody VλCDR3 amino acid sequences comprising about 1 to about 10 ofthe amino acids found at Kabat positions 89, 90, 91, 92, 93, 94, 95,95A, 95B, 95C, 96, and 97, in selected VλCDR3 sequences encoded by asingle germline sequence.

In some embodiments, the invention relates to a library of syntheticpolynucleotides encoding a plurality of antibody CDRH3 amino acidsequences, wherein the library has a theoretical total diversity ofabout 10⁶ to about 10¹⁵ unique CDRH3 sequences.

In still other embodiments, the invention relates to a method ofpreparing a library of synthetic polynucleotides encoding a plurality ofantibody VK amino acid sequences, the method comprising:

(i) providing polynucleotide sequences encoding:

-   -   (a) one or more VK_Chassis amino acid sequences selected from        the group consisting of about Kabat amino acid 1 to about Kabat        amino acid 88 encoded by IGKV1-05 (SEQ ID NO: 229), IGKV1-06        (SEQ ID NO: 451), IGKV1-08 (SEQ ID NO: 452, 453), IGKV1-09 (SEQ        ID NO: 454), IGKV1-12 (SEQ ID NO: 230), IGKV1-13 (SEQ ID NO:        455), IGKV1-16 (SEQ ID NO: 456), IGKV1-17 (SEQ ID NO: 457),        IGKV1-27 (SEQ ID NO: 231), IGKV1-33 (SEQ ID NO: 232), IGKV1-37        (SEQ ID NOs: 458, 459), IGKV1-39 (SEQ ID NO: 233), IGKV1D-16        (SEQ ID NO: 460), IGKV1D-17 (SEQ ID NO: 461), IGKV1D-43 (SEQ ID        NO: 462), IGKV1D-8 (SEQ ID NOs: 463, 464), IGKV2-24 (SEQ ID NO:        465), IGKV2-28 (SEQ ID NO: 234), IGKV2-29 (SEQ ID NO: 466),        IGKV2-30 (SEQ ID NO: 467), IGKV2-40 (SEQ ID NO: 468), IGKV2D-26        (SEQ ID NO: 469), IGKV2D-29 (SEQ ID NO: 470), IGKV2D-30 (SEQ ID        NO: 471), IGKV3-11 (SEQ ID NO: 235), IGKV3-15 (SEQ ID NO: 236),        IGKV3-20 (SEQ ID NO: 237), IGKV3D-07 (SEQ ID NO: 472), IGKV3D-11        (SEQ ID NO: 473), IGKV3D-20 (SEQ ID NO: 474), IGKV4-1 (SEQ ID        NO: 238), IGKV5-2 (SEQ ID NOs: 475, 476), IGKV6-21 (SEQ ID NOs:        477), and IGKV6D-41, or a sequence at least about 80% identical        to any of them;

(b) one or more L3-VK amino acid sequences, wherein L3-VK the portion ofthe VKCDR3 amino acid sequence encoded by the IGKV gene segment;

(c) one or more X residues, wherein X is any amino acid residue; and

(d) one or more JK* amino acid sequences, wherein JK* is an amino acidsequence selected from the group consisting amino acid sequences encodedby IGKJ1 (SEQ ID NO: 552), IGKJ2 (SEQ ID NO: 553), IGKJ3 (SEQ ID NO:554), IGKJ4 (SEQ ID NO: 555), and IGKJ5 (SEQ ID NO: 556), wherein thefirst amino acid residue of each sequence is not present; and

(ii) assembling the polynucleotide sequences to produce a library ofsynthetic polynucleotides encoding a plurality of human VK sequencesrepresented by the following formula:

[VK_Chassis]-[L3-VK]-[X]-[JK*].

In some embodiments, the invention relates to a method of preparing alibrary of synthetic polynucleotides encoding a plurality of antibodylight chain CDR3 sequences, the method comprising:

(i) determining the percent occurrence of each amino acid residue ateach position in selected light chain CDR3 amino acid sequences derivedfrom a single germline polynucleotide sequence;

(ii) designing synthetic polynucleotides encoding a plurality of humanantibody light chain CDR3 amino acid sequences, wherein the percentoccurrence of any amino acid at any position within the designed lightchain CDR3 amino acid sequences is within at least about 30% of thepercent occurrence in the selected light chain CDR3 amino acid sequencesderived from a single germline polynucleotide sequence, as determined in(i); and

(iii) synthesizing one or more polynucleotides that were designed in(ii).

In other embodiments, the invention relates to a method of preparing alibrary of synthetic polynucleotides encoding a plurality of antibody Vλamino acid sequences, the method comprising:

(i) providing polynucleotide sequences encoding:

-   -   (a) one or more Vλ_Chassis amino acid sequences selected from        the group consisting of about Kabat residue 1 to about Kabat        residue 88 encoded by IGλV1-36 SEQ ID NO: 480), IGλV1-40 (SEQ ID        NO: 531), IGλV1-44 (SEQ ID NO: 532), IGλV1-47 (SEQ ID NO: 481),        IGλV1-51 (SEQ ID NO: 533), IGλV10-54 (SEQ ID NO: 482), IGλV2-11        (SEQ ID NO: 483, 484), IGλV2-14 (SEQ ID NO: 534), IGλV2-18 (SEQ        ID NO: 485), IGλV2-23 (SEQ ID NO: 486, 487), IGλV2-8 (SEQ ID NO:        488), IGλV3-1 (SEQ ID NO: 535), IGλV3-10 (SEQ ID NO: 489),        IGλV3-12 (SEQ ID NO: 490), IGλV3-16 (SEQ ID NO: 491), IGλV3-19        (SEQ ID NO: 536), IGλV3-21 (SEQ ID NO: 537), IGλV3-25 (SEQ ID        NO: 492), IGλV3-27 (SEQ ID NO: 493), IGλV3-9 (SEQ ID NO: 494),        IGλV4-3 (SEQ ID NO: 495), IGλV4-60 (SEQ ID NO: 496), IGλV4-69        (SEQ ID NO: 538), IGλV5-39 (SEQ ID NO: 497), IGλV5-45 (SEQ ID        NO: 540), IGλV6-57 (SEQ ID NO: 539), IGλV7-43 (SEQ ID NO: 541),        IGλV7-46 (SEQ ID NO: 498), IGλV8-61 (SEQ ID NO: 499), IGλV9-49        (SEQ ID NO: 500), and IGλV10-54 (SEQ ID NO: 482), or a sequence        at least about 80% identical to any of them;

(b) one or more L3-Vλ sequences, wherein L3-Vλ is the portion of theVλCDR3 amino acid sequence encoded by the IGλV gene segment;

(c) one or more Jλ sequences, wherein Jλ is an amino acid sequenceselected from the group consisting of amino acid sequences encoded byIGλJ1-01 (SEQ ID NO: 557), IGλJ2-01 (SEQ ID NO: 558), IGλJ3-01 (SEQ IDNO: 559), IGλJ3-02 (SEQ ID NO: 560), IGλJ6-01 (SEQ ID NO: 561), IGλJ7-01(SEQ ID NO: 562), and IGλJ7-02 (SEQ ID NO: 563) wherein the first aminoacid residue of each sequence may or may not be present; and

(ii) assembling the polynucleotide sequences to produce a library ofsynthetic polynucleotides encoding a plurality of human Vλ amino acidsequences represented by the following formula:

[Vλ_Chassis]-[L3-Vλ]-[Jλ].

In certain embodiments, the amino acid sequences encoded by thepolynucleotides of the libraries of the invention are human.

The present invention is also directed to methods of preparing asynthetic polynucleotide library comprising providing and assembling thepolynucleotide sequences of the instant invention.

In another aspect, the invention comprises a method of preparing thelibrary of synthetic polynucleotides encoding a plurality of antibodyCDRH3 amino acid sequences, the method comprising:

-   -   (i) providing polynucleotide sequences encoding:        -   (a) one or more N1 amino acid sequences of about 0 to about            3 amino acids, wherein each amino acid of the N1 amino acid            sequence is among the 12 most frequently occurring amino            acids at the corresponding position in N1 sequences of CDRH3            amino acid sequences that are functionally expressed by            human B cells;        -   (b) one or more human CDRH3 DH amino acid sequences, N- and            C-terminal truncations thereof, or a sequence of at least            about 80% identity to any of them;        -   (c) one or more N2 amino acid sequences of about 0 to about            3 amino acids, wherein each amino acid of the N1 amino acid            sequence is among the 12 most frequently occurring amino            acids at the corresponding position in N2 amino acid            sequences of CDRH3 amino acid sequences that are            functionally expressed by human B cells; and        -   (d) one or more human CDRH3 H3-JH amino acid sequences,            N-terminal truncations thereof, or a sequence of at least            about 80% identity to any of them; and    -   (ii) assembling the polynucleotide sequences to produce a        library of synthetic polynucleotides encoding a plurality of        human antibody CDRH3 amino acid sequences represented by the        following formula:

[N1]-[DH]-[N2]-[H3-JH].

In one aspect, one or more of the polynucleotide sequences aresynthesized via split-pool synthesis.

In another aspect, the method of the invention further comprises thestep of recombining the assembled synthetic polynucleotides with avector comprising a heavy chain chassis and a heavy chain constantregion, to form a full-length heavy chain.

In another aspect, the method of the invention further comprises thestep of providing a 5′ polynucleotide sequence and a 3′ polynucleotidesequence that facilitate homologous recombination. In still anotheraspect, the method of the invention further comprises the step ofrecombining the assembled synthetic polynucleotides with a vectorcomprising a heavy chain chassis and a heavy chain constant region, toform a full-length heavy chain.

In some embodiments, the step of recombining is performed in yeast. Incertain embodiments, the yeast is S. cerevisiae.

In certain other embodiments, the invention comprises a method ofisolating one or more host cells expressing one or more antibodies, themethod comprising:

-   -   (i) expressing the human antibodies of any one of claims 40 and        46 in one or more host cells;    -   (ii) contacting the host cells with one or more antigens; and    -   (iii) isolating one or more host cells having antibodies that        bind to the one or more antigens.

In another aspect, the method of the invention further comprises thestep of isolating one or more antibodies from the one or more host cellsthat present the antibodies which recognize the one or more antigens. Inyet another aspect, the method of the invention further comprises thestep of isolating one or more polynucleotide sequences encoding one ormore antibodies from the one or more host cells that present theantibodies which recognize the one or more antigens.

In certain other embodiments, the invention comprises a kit comprisingthe library of synthetic polynucleotides encoding a plurality ofantibody CDRH3 amino acid sequences, or any of the other sequencesdisclosed herein.

In still other aspects, the CDRH3 amino acid sequences encoded by thelibraries of synthetic polynucleotides described herein, or any of theother sequences disclosed herein, are in computer readable form.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a schematic of recombination between a fragment (e.g.,CDR3) and a vector (e.g., comprising a chassis and constant region) forthe construction of a library.

FIG. 2 depicts the length distribution of the N1 and N2 regions ofrearranged human antibody sequences compiled from Jackson et al. (J.Immunol Methods, 2007, 324: 26, incorporated by reference in itsentirety).

FIG. 3 depicts the length distribution of the CDRL3 regions ofrearranged human kappa light chain sequences compiled from the NCBIdatabase (Appendix A).

FIG. 4 depicts the length distribution of the CDRL3 regions ofrearranged human lambda light chain sequences compiled from the NCBIdatabase (Appendix B).

FIG. 5 depicts a schematic representation of the 424 cloning vectorsused in the synthesis of the CDRH3 regions before and after ligation ofthe [DH]-[N2]-[JH] segment (DTAVYYCAR: SEQ ID NO: 579; DTAVYYCAK: SEQ IDNO: 578; SSASTK: SEQ ID NO: 580).

FIG. 6 depicts a schematic structure of a heavy chain vector, prior torecombination with a CDRH3.

FIGS. 7A and 7B depict a schematic diagram of a CDRH3 integrated into aheavy chain vector and the polynucleotide and polypeptide sequences ofCDRH3 (SEQ ID NO: 581).

FIG. 8 depicts a schematic structure of a kappa light chain vector,prior to recombination with a CDRL3.

FIGS. 9A and 9B depict a schematic diagram of a CDRL3 integrated into alight chain vector and the polynucleotide and polypeptide sequences ofCDRL3 (SEQ ID NO: 582).

FIG. 10 depicts the length distribution of the CDRH3 domain (Kabatpositions 95-102) from 96 colonies obtained by transformation with 10 ofthe 424 vectors synthesized as described in Example 10 (observed), ascompared to the expected (i.e., designed) distribution.

FIG. 11 depicts the length distribution of the DH segment from 96colonies obtained by transformation with 10 of the 424 vectorssynthesized as described in Example 10 (observed), as compared to theexpected (i.e., designed) distribution.

FIG. 12 depicts the length distribution of the N2 segment from 96colonies obtained by transformation with 10 of the 424 vectorssynthesized as described in Example 10 (observed), as compared to theexpected (i.e., designed) distribution.

FIG. 13 depicts the length distribution of the H3-JH segment from 96colonies obtained by transformation with 10 of the 424 vectorssynthesized as described in Example 10 (observed), as compared to theexpected (i.e., designed) distribution.

FIG. 14 depicts the length distribution of the CDRH3 domains from 291sequences prepared from yeast cells transformed according to the methodoutlined in Example 10.4, namely the co-transformation of vectorscontaining heavy chain chassis and constant regions with a CDRH3 insert(observed), as compared to the expected (i.e., designed) distribution.

FIG. 15 depicts the length distribution of the [Tail]-[N1] region fromthe 291 sequences prepared from yeast cells transformed according to theprotocol outlined in Example 10.4 (observed), as compared to theexpected (i.e., designed) distribution.

FIG. 16 depicts the length distribution of the DH region from the 291sequences prepared from yeast cells transformed according to theprotocol outlined in Example 10.4 (observed), as compared to thetheoretical (i.e., designed) distribution.

FIG. 17 depicts the length distribution of the N2 region from the 291sequences prepared from yeast cells transformed according to theprotocol outlined in Example 10.4 (observed), as compared to thetheoretical (i.e., designed) distribution.

FIG. 18 depicts the length distribution of the H3-JH region from the 291sequences prepared from yeast cells transformed according to theprotocol outlined in Example 10.4 (observed), as compared to thetheoretical (i.e., designed) distribution.

FIG. 19 depicts the familial origin of the JH segments identified in the291 sequences (observed), as compared to the theoretical (i.e.,designed) familial origin.

FIG. 20 depicts the representation of each of the 16 chassis of thelibrary (observed), as compared to the theoretical (i.e., designed)chassis representation. VH3-23 is represented twice; once ending in CARand once ending in CAK. These representations were combined, as were theten variants of VH3-33 with one variant of VH3-30.

FIG. 21 depicts a comparison of the CDRL3 length from 86 sequencesselected from the VKCDR3 library of Example 6.2 (observed) to humansequences (human) and the designed sequences (designed).

FIG. 22 depicts the representation of the light chain chassis amongstthe 86 sequences selected from the library (observed), as compared tothe theoretical (i.e., designed) chassis representation.

FIG. 23 depicts the frequency of occurrence of different CDRH3 lengthsin an exemplary library of the invention, versus the preimmunerepertoire of Lee et al. (Immunogenetics, 2006, 57: 917, incorporated byreference in its entirety).

FIG. 24 depicts binding curves for 6 antibodies selected from a libraryof the invention.

FIG. 25 depicts binding curves for 10 antibodies selected from a libraryof the invention binding to hen egg white lysozyme.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to, at least, synthetic polynucleotidelibraries, methods of producing and using the libraries of theinvention, kits and computer readable forms including the libraries ofthe invention. The libraries taught in this application are described,at least in part, in terms of the components from which they areassembled.

In certain embodiments, the instant invention provides antibodylibraries specifically designed based on the composition and CDR lengthdistribution in the naturally occurring human antibody repertoire. It isestimated that, even in the absence of antigenic stimulation, a humanmakes at least about 10⁷ different antibody molecules. Theantigen-binding sites of many antibodies can cross-react with a varietyof related but different epitopes. In addition the human antibodyrepertoire is large enough to ensure that there is an antigen-bindingsite to fit almost any potential epitope, albeit with low affinity.

The mammalian immune system has evolved unique genetic mechanisms thatenable it to generate an almost unlimited number of different light andheavy chains in a remarkably economical way, by combinatorially joiningchromosomally separated gene segments prior to transcription. Each typeof immunoglobulin (Ig) chain (i.e., κ light, λ light, and heavy) issynthesized by combinatorial assembly of DNA sequences selected from twoor more families of gene segments, to produce a single polypeptidechain. Specifically, the heavy chains and light chains each consist of avariable region and a constant (C) region. The variable regions of theheavy chains are encoded by DNA sequences assembled from three familiesof gene segments: variable (IGHV), joining (IGHJ) and diversity (IGHD).The variable regions of light chains are encoded by DNA sequencesassembled from two families of gene segments for each of the kappa andlambda light chains: variable (IGLV) and joining (IGLJ). Each variableregion (heavy and light) is also recombined with a constant region, toproduce a full-length immunoglobulin chain.

While combinatorial assembly of the V, D and J gene segments make asubstantial contribution to antibody variable region diversity, furtherdiversity is introduced in vivo, at the pre-B cell stage, via imprecisejoining of these gene segments and the introduction of non-templatednucleotides at the junctions between the gene segments.

After a B cell recognizes an antigen, it is induced to proliferate.During proliferation, the B cell receptor locus undergoes an extremelyhigh rate of somatic mutation that is far greater than the normal rateof genomic mutation. The mutations that occur are primarily localized tothe Ig variable regions and comprise substitutions, insertions anddeletions. This somatic hypermutation enables the production of B cellsthat express antibodies possessing enhanced affinity toward an antigen.Such antigen-driven somatic hypermutation fine-tunes antibody responsesto a given antigen.

Significant efforts have been made to create antibody libraries withextensive diversity, and to mimic the natural process of affinitymaturation of antibodies against various antigens, especially antigensassociated with diseases such as autoimmune diseases, cancer, andinfectious disease. Antibody libraries comprising candidate bindingmolecules that can be readily screened against targets are desirable.However, the full promise of an antibody library, which isrepresentative of the preimmune human antibody repertoire, has remainedelusive. In addition to the shortcomings enumerated above, andthroughout the application, synthetic libraries that are known in theart often suffer from noise (i.e., very large libraries increase thepresence of many sequences which do not express well, and/or whichmisfold), while entirely human libraries that are known in the art maybe biased against certain antigen classes (e.g., self-antigens).Moreover, the limitations of synthesis and physical realizationtechniques restrict the functional diversity of antibody libraries ofthe art. The present invention provides, for the first time, a fullysynthetic antibody library that is representative of the human preimmuneantibody repertoire (e.g., in composition and length), and that can bereadily screened (i.e., it is physically realizable and, in some casescan be oversampled) using, for example, high throughput methods, toobtain, for example, new therapeutics and/or diagnostics

In particular, the synthetic antibody libraries of the instant inventionhave the potential to recognize any antigen, including self-antigens ofhuman origin. The ability to recognize self-antigens is usually lost inan expressed human library, because self-reactive antibodies are removedby the donor's immune system via negative selection. Another feature ofthe invention is that screening the antibody library using positiveclone selection, for example, by FACS (florescence activated cellsorter) bypasses the standard and tedious methodology of generating ahybridoma library and supernatant screening. Still further, thelibraries, or sub-libraries thereof, can be screened multiple times, todiscover additional antibodies against other desired targets.

Before further description of the invention, certain terms are defined.

1. DEFINITIONS

Unless defined otherwise, all technical and scientific terms used hereinhave the meaning commonly understood by one of ordinary skill in the artrelevant to the invention. The definitions below supplement those in theart and are directed to the embodiments described in the currentapplication.

The term “antibody” is used herein in the broadest sense andspecifically encompasses at least monoclonal antibodies, polyclonalantibodies, multi-specific antibodies (e.g., bispecific antibodies),chimeric antibodies, humanized antibodies, human antibodies, andantibody fragments. An antibody is a protein comprising one or morepolypeptides substantially or partially encoded by immunoglobulin genesor fragments of immunoglobulin genes. The recognized immunoglobulingenes include the kappa, lambda, alpha, gamma, delta, epsilon and muconstant region genes, as well as myriad immunoglobulin variable regiongenes.

“Antibody fragments” comprise a portion of an intact antibody, forexample, one or more portions of the antigen-binding region thereof.Examples of antibody fragments include Fab, Fab′, F(ab′)₂, and Fvfragments, diabodies, linear antibodies, single-chain antibodies, andmulti-specific antibodies formed from intact antibodies and antibodyfragments.

An “intact antibody” is one comprising full-length heavy- andlight-chains and an Fc region. An intact antibody is also referred to asa “full-length, heterodimeric” antibody or immunoglobulin.

The term “variable” refers to the portions of the immunoglobulin domainsthat exhibit variability in their sequence and that are involved indetermining the specificity and binding affinity of a particularantibody (i.e., the “variable domain(s)”). Variability is not evenlydistributed throughout the variable domains of antibodies; it isconcentrated in sub-domains of each of the heavy and light chainvariable regions. These sub-domains are called “hypervariable” regionsor “complementarity determining regions” (CDRs). The more conserved(i.e., non-hypervariable) portions of the variable domains are calledthe “framework” regions (FRM). The variable domains of naturallyoccurring heavy and light chains each comprise four FRM regions, largelyadopting a β-sheet configuration, connected by three hypervariableregions, which form loops connecting, and in some cases forming part of,the β-sheet structure. The hypervariable regions in each chain are heldtogether in close proximity by the FRM and, with the hypervariableregions from the other chain, contribute to the formation of theantigen-binding site (see Kabat et al. Sequences of Proteins ofImmunological Interest, 5th Ed. Public Health Service, NationalInstitutes of Health, Bethesda, Md., 1991, incorporated by reference inits entirety). The constant domains are not directly involved in antigenbinding, but exhibit various effector functions, such as, for example,antibody-dependent, cell-mediated cytotoxicity and complementactivation.

The “chassis” of the invention represent a portion of the antibody heavychain variable (IGHV) or light chain variable (IGLV) domains that arenot part of CDRH3 or CDRL3, respectively. The chassis of the inventionis defined as the portion of the variable region of an antibodybeginning with the first amino acid of FRM1 and ending with the lastamino acid of FRM3. In the case of the heavy chain, the chassis includesthe amino acids including from about Kabat position 1 to about Kabatposition 94. In the case of the light chains (kappa and lambda), thechassis are defined as including from about Kabat position 1 to aboutKabat position 88. The chassis of the invention may contain certainmodifications relative to the corresponding germline variable domainsequences presented herein or available in public databases. Thesemodifications may be engineered (e.g., to remove N-linked glycosylationsites) or naturally occurring (e.g., to account for allelic variation).For example, it is known in the art that the immunoglobulin generepertoire is polymorphic (Wang et al., Immunol. Cell. Biol., 2008, 86:111; Collins et al., Immunogenetics, 2008, DOI10.1007/s00251-008-0325-z, published online, each incorporated byreference in its entirety); chassis, CDRs (e.g., CDRH3) and constantregions representative of these allelic variants are also encompassed bythe invention. In some embodiments, the allelic variant(s) used in aparticular embodiment of the invention may be selected based on theallelic variation present in different patient populations, for example,to identify antibodies that are non-immunogenic in these patientpopulations. In certain embodiments, the immunogenicity of an antibodyof the invention may depend on allelic variation in the majorhistocompatibility complex (MHC) genes of a patient population. Suchallelic variation may also be considered in the design of libraries ofthe invention. In certain embodiments of the invention, the chassis andconstant regions are contained on a vector, and a CDR3 region isintroduced between them via homologous recombination.

In some embodiments, one, two or three nucleotides may follow the heavychain chassis, forming either a partial (if one or two) or a complete(if three) codon. When a full codon is present, these nucleotides encodean amino acid residue that is referred to as the “tail,” and occupiesposition 95.

The “CDRH3 numbering system” used herein defines the first amino acid ofCDRH3 as being at Kabat position 95 (the “tail,” when present) and thelast amino acid of CDRH3 as position 102. The amino acids following the“tail” are called “N1” and, when present, are assigned numbers 96, 96A,96B, etc. The N1 segment is followed by the “DH” segment, which isassigned numbers 97, 97A, 97B, 97C, etc. The DH segment is followed bythe “N2” segment, which, when present, is numbered 98, 98A, 98B, etc.Finally, the most C-terminal amino acid residue of the set of the“H3-JH” segment is designated as number 102. The residue directly before(N-terminal) it, when present, is 101, and the one before (if present)is 100. For reasons of convenience, and which will become apparentelsewhere, the rest of the H3-JH amino acids are numbered in reverseorder, beginning with 99 for the amino acid just N-terminal to 100, 99Afor the residue N-terminal to 99, and so forth for 99B, 99C, etc.Examples of certain CDRH3 sequence residue numbers may therefore includethe following:

As used herein, the term “diversity” refers to a variety or a noticeableheterogeneity. The term “sequence diversity” refers to a variety ofsequences which are collectively representative of several possibilitiesof sequences, for example, those found in natural human antibodies. Forexample, heavy chain CDR3 (CDRH3) sequence diversity may refer to avariety of possibilities of combining the known human DH and H3-JHsegments, including the N1 and N2 regions, to form heavy chain CDR3sequences. The light chain CDR3 (CDRL3) sequence diversity may refer toa variety of possibilities of combining the naturally occurring lightchain variable region contributing to CDRL3 (i.e., L3-VL) and joining(i.e., L3-JL) segments, to form light chain CDR3 sequences. As usedherein, H3-JH refers to the portion of the IGHJ gene contributing toCDRH3. As used herein, L3-VL and L3-JL refer to the portions of the IGLVand IGLJ genes (kappa or lambda) contributing to CDRL3, respectively.

As used herein, the term “expression” includes any step involved in theproduction of a polypeptide including, but not limited to,transcription, post-transcriptional modification, translation,post-translational modification, and secretion.

As used herein, the term “host cell” is intended to refer to a cell intowhich a polynucleotide of the invention. It should be understood thatsuch terms refer not only to the particular subject cell but to theprogeny or potential progeny of such a cell. Because certainmodifications may occur in succeeding generations due to either mutationor environmental influences, such progeny may not, in fact, be identicalto the parent cell, but are still included within the scope of the termas used herein.

The term “length diversity” refers to a variety in the length of aparticular nucleotide or amino acid sequence. For example, in naturallyoccurring human antibodies, the heavy chain CDR3 sequence varies inlength, for example, from about 3 amino acids to over about 35 aminoacids, and the light chain CDR3 sequence varies in length, for example,from about 5 to about 16 amino acids. Prior to the instant invention, itwas known in the art that it is possible to design antibody librariescontaining sequence diversity or length diversity (see, e.g., Hoet etal., Nat. Biotechnol., 2005, 23: 344; Kretzschmar and von Ruden, Curr.Opin. Biotechnol., 2002 13: 598; and Rauchenberger et al., J. Biol.Chem., 2003 278: 38194, each of which is incorporated by reference inits entirety); however, the instant invention is directed to, at least,the design of synthetic antibody libraries containing the sequencediversity and length diversity of naturally occurring human sequences.In some cases, synthetic libraries containing sequence and lengthdiversity have been synthesized, however these libraries contain toomuch theoretical diversity to synthesize the entire designed repertoireand/or too many theoretical members to physically realize or oversamplethe entire library.

As used herein, a sequence designed with “directed diversity” has beenspecifically designed to contain both sequence diversity and lengthdiversity. Directed diversity is not stochastic.

As used herein, “stochastic” describes a process of generating arandomly determined sequence of amino acids, which is considered as asample of one element from a probability distribution.

The term “library of polynucleotides” refers to two or morepolynucleotides having a diversity as described herein, specificallydesigned according to the methods of the invention. The term “library ofpolypeptides” refers to two or more polypeptides having a diversity asdescribed herein, specifically designed according to the methods of theinvention. The term “library of synthetic polynucleotides” refers to apolynucleotide library that includes synthetic polynucleotides. The term“library of vectors” refers herein to a library of at least twodifferent vectors. As used herein, the term “human antibody libraries,”at least includes, a polynucleotide or polypeptide library which hasbeen designed to represent the sequence diversity and length diversityof naturally occurring human antibodies.

As described throughout the specification, the term “library” is usedherein in its broadest sense, and also may include the sub-librariesthat may or may not be combined to produce libraries of the invention.

As used herein, the term “synthetic polynucleotide” refers to a moleculeformed through a chemical process, as opposed to molecules of naturalorigin, or molecules derived via template-based amplification ofmolecules of natural origin (e.g., immunoglobulin chains cloned frompopulations of B cells via PCR amplification are not “synthetic” usedherein). In some instances, for example, when referring to libraries ofthe invention that comprise multiple components (e.g., N1, DH, N2,and/or H3-JH), the invention encompasses libraries in which at least oneof the aforementioned components is synthetic. By way of illustration, alibrary in which certain components are synthetic, while othercomponents are of natural origin or derived via template-basedamplification of molecules of natural origin, would be encompassed bythe invention.

The term “split-pool synthesis” refers to a procedure in which theproducts of a plurality of first reactions are combined (pooled) andthen separated (split) before participating in a plurality of secondreactions. Example 9, describes the synthesis of 278 DH segments(products), each in a separate reaction. After synthesis, these 278segments are combined (pooled) and then distributed (split) amongst 141columns for the synthesis of the N2 segments. This enables the pairingof each of the 278 DH segments with each of the 141 N2 segments. Asdescribed elsewhere in the specification, these numbers arenon-limiting.

“Preimmune” antibody libraries have similar sequence diversities andlength diversities to naturally occurring human antibody sequencesbefore these sequences have undergone negative selection or somatichypermutation. For example, the set of sequences described in Lee et al.(Immunogenetics, 2006, 57: 917, incorporated by reference in itsentirety) is believed to represent sequences from the preimmunerepertoire. In certain embodiments of the invention, the sequences ofthe invention will be similar to these sequences (e.g., in terms ofcomposition and length). In certain embodiments of the invention, suchantibody libraries are designed to be small enough to chemicallysynthesize and physically realize, but large enough to encode antibodieswith the potential to recognize any antigen. In one embodiment of theinvention, an antibody library comprises about 10⁷ to about 10²⁰different antibodies and/or polynucleotide sequences encoding theantibodies of the library. In some embodiments, the libraries of theinstant invention are designed to include 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸,10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹, or 10²⁰different antibodies and/or polynucleotide sequences encoding theantibodies. In certain embodiments, the libraries of the invention maycomprise or encode about 10³ to about 10⁵, about 10⁵ to about 10⁷, about10⁷ to about 10⁹, about 10⁹ to about 10¹¹, about 10¹¹ to about 10¹³,about 10¹³ to about 10¹⁵, about 10¹⁵ to about 10¹⁷, or about 10¹⁷ toabout 10²⁰ different antibodies. In certain embodiments of theinvention, the diversity of the libraries may be characterized as beinggreater than or less than one or more of the diversities enumeratedabove, for example greater than about 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹,10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹, or, 10²⁰ orless than about 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹²,10¹³, 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹, or 10²⁰. In certain otherembodiments of the invention, the probability of an antibody of interestbeing present in a physical realization of a library with a size asenumerated above is at least about 0.0001%, 0.001%, 0.01%, 0.1%, 1%, 5%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 99%, 99.5%, or99.9% (see Library Sampling, in the Detailed Description, for moreinformation on the probability of a particular sequence being present ina physical realization of a library). The antibody libraries of theinvention may also include antibodies directed to, for example, self(i.e., human) antigens. The antibodies of the present invention may notbe present in expressed human libraries for reasons including becauseself-reactive antibodies are removed by the donor's immune system vianegative selection. However, novel heavy/light chain pairings may insome cases create self-reactive antibody specificity (Griffiths et al.U.S. Pat. No. 5,885,793, incorporated by reference in its entirety). Incertain embodiments of the invention, the number of unique heavy chainsin a library may be about 10, 50, 10², 150, 10³, 10⁴, 10⁵, 10⁶, 10⁷,10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹,10²⁰, or more. In certain embodiments of the invention, the number ofunique light chains in a library may be about 5, 10, 25, 50, 10², 150,500, 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴,10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹, 10²⁰, or more.

As used herein, the term “human antibody CDRH3 libraries,” at leastincludes, a polynucleotide or polypeptide library which has beendesigned to represent the sequence diversity and length diversity ofnaturally occurring human antibodies. “Preimmune” CDRH3 libraries havesimilar sequence diversities and length diversities to naturallyoccurring human antibody CDRH3 sequences before these sequences undergonegative selection and somatic hypermutation. Known human CDRH3sequences are represented in various data sets, including Jackson etal., J. Immunol. Methods, 2007, 324: 26; Martin, Proteins, 1996, 25:130; and Lee et al., Immunogenetics, 2006, 57: 917, each of which isincorporated by reference in its entirety. In certain embodiments of theinvention, such CDRH3 libraries are designed to be small enough tochemically synthesize and physically realize, but large enough to encodeCDRH3s with the potential to recognize any antigen. In one embodiment ofthe invention, an antibody library includes about 10⁶ to about 10¹⁵different CDRH3 sequences and/or polynucleotide sequences encoding saidCDRH3 sequences. In some embodiments, the libraries of the instantinvention are designed to about 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, or 10¹⁶, different CDRH3 sequencesand/or polynucleotide sequences encoding said CDRH3 sequences. In someembodiments, the libraries of the invention may include or encode about10³ to about 10⁶, about 10⁶ to about 10⁸, about 10⁸ to about 10¹⁰, about10¹⁰ to about 10¹², about 10¹² to about 10¹⁴, or about 10¹⁴ to about10¹⁶ different CDRH3 sequences. In certain embodiments of the invention,the diversity of the libraries may be characterized as being greaterthan or less than one or more of the diversities enumerated above, forexample greater than about 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰,10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, or 10¹⁶ or less than about 10³, 10⁴, 10⁵,10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵ or 10¹⁶. Incertain embodiments of the invention, the probability of a CDRH3 ofinterest being present in a physical realization of a library with asize as enumerated above is at least about 0.0001%, 0.001%, 0.01%, 0.1%,1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 40%, 50%,60%, 70%, 80%, 85%, 90%, 95%, 99%, 99.5%, or 99.9% (see LibrarySampling, in the Detailed Description, for more information on theprobability of a particular sequence being present in a physicalrealization of a library). The preimmune CDRH3 libraries of theinvention may also include CDRH3s directed to, for example, self (i.e.,human) antigens. Such CDRH3s may not be present in expressed humanlibraries, because self-reactive CDRH3s are removed by the donor'simmune system via negative selection.

Libraries of the invention containing “VKCDR3” sequences and “VλCDR3”sequences refer to the kappa and lambda sub-sets of the CDRL3 sequences,respectively. These libraries may be designed with directed diversity,to collectively represent the length and sequence diversity of the humanantibody CDRL3 repertoire. “Preimmune” versions of these libraries havesimilar sequence diversities and length diversities to naturallyoccurring human antibody CDRL3 sequences before these sequences undergonegative selection. Known human CDRL3 sequences are represented invarious data sets, including the NCBI database (see Appendix A andAppendix B for light chain sequence data sets) and Martin, Proteins,1996, 25: 130 incorporated by reference in its entirety. In certainembodiments of the invention, such CDRL3 libraries are designed to besmall enough to chemically synthesize and physically realize, but largeenough to encode CDRL3s with the potential to recognize any antigen.

In one embodiment of the invention, an antibody library comprises about10⁵ different CDRL3 sequences and/or polynucleotide sequences encodingsaid CDRL3 sequences. In some embodiments, the libraries of the instantinvention are designed to comprise about 10¹, 10², 10³, 10⁴, 10⁶, 10⁷,or 10⁸ different CDRL3 sequences and/or polynucleotide sequencesencoding said CDRL3 sequences. In some embodiments, the libraries of theinvention may comprise or encode about 10¹ to about 10³, about 10³ toabout 10⁵, or about 10⁵ to about 10⁸ different CDRL3 sequences. Incertain embodiments of the invention, the diversity of the libraries maybe characterized as being greater than or less than one or more of thediversities enumerated above, for example greater than about 10¹, 10²,10³, 10⁴, 10⁵, 10⁶, 10⁷, or 10⁸ or less than about 10¹, 10², 10³, 10⁴,10⁵, 10⁶, 10⁷, or 10⁸. In certain embodiments of the invention, theprobability of a CDRL3 of interest being present in a physicalrealization of a library with a size as enumerated above is at leastabout 0.0001%, 0.001%, 0.01%, 0.1%, 1%, 5%, 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 85%, 90%, 95%, 99%, 99.5%, or 99.9% (see LibrarySampling, in the Detailed Description, for more information on theprobability of a particular sequence being present in a physicalrealization of a library). The preimmune CDRL3 libraries of theinvention may also include CDRL3s directed to, for example, self (i.e.,human) antigens. Such CDRL3s may not be present in expressed humanlibraries, because self-reactive CDRL3s are removed by the donor'simmune system via negative selection.

As used herein, the term “known heavy chain CDR3 sequences” refers toheavy chain CDR3 sequences in the public domain that have been clonedfrom populations of human B cells. Examples of such sequences are thosepublished or derived from public data sets, including, for example,Zemlin et al., JMB, 2003, 334: 733; Lee et al., Immunogenetics, 2006,57: 917; and Jackson et al. J. Immunol. Methods, 2007, 324: 26, each ofwhich are incorporated by reference in their entirety.

As used herein, the term “known light chain CDR3 sequences” refers tolight chain CDR3 sequences (e.g., kappa or lambda) in the public domainthat have been cloned from populations of human B cells. Examples ofsuch sequences are those published or derived from public data sets,including, for example, the NCBI database (see Appendices A and B filedherewith).

As used herein the term “antibody binding regions” refers to one or moreportions of an immunoglobulin or antibody variable region capable ofbinding an antigen(s). Typically, the antibody binding region is, forexample, an antibody light chain (or variable region or one or more CDRsthereof), an antibody heavy chain (or variable region or one or moreCDRs thereof), a heavy chain Fd region, a combined antibody light andheavy chain (or variable regions thereof) such as a Fab, F(ab′)₂, singledomain, or single chain antibodies (scFv), or any region of a fulllength antibody that recognizes an antigen, for example, an IgG (e.g.,an IgG1, IgG2, IgG3, or IgG4 subtype), IgA1, IgA2, IgD, IgE, or IgMantibody.

The term “framework region” refers to the art-recognized portions of anantibody variable region that exist between the more divergent (i.e.,hypervariable) CDRs. Such framework regions are typically referred to asframeworks 1 through 4 (FRM1, FRM2, FRM3, and FRM4) and provide ascaffold for the presentation of the six CDRs (three from the heavychain and three from the light chain) in three dimensional space, toform an antigen-binding surface.

The term “canonical structure” refers to the main chain conformationthat is adopted by the antigen binding (CDR) loops. From comparativestructural studies, it has been found that five of the six antigenbinding loops have only a limited repertoire of available conformations.Each canonical structure can be characterized by the torsion angles ofthe polypeptide backbone. Correspondent loops between antibodies may,therefore, have very similar three dimensional structures, despite highamino acid sequence variability in most parts of the loops (Chothia andLesk, J. Mol. Biol., 1987, 196: 901; Chothia et al., Nature, 1989, 342:877; Martin and Thornton, J. Mol. Biol., 1996, 263: 800, each of whichis incorporated by reference in its entirety). Furthermore, there is arelationship between the adopted loop structure and the amino acidsequences surrounding it. The conformation of a particular canonicalclass is determined by the length of the loop and the amino acidresidues residing at key positions within the loop, as well as withinthe conserved framework (i.e., outside of the loop). Assignment to aparticular canonical class can therefore be made based on the presenceof these key amino acid residues. The term “canonical structure” mayalso include considerations as to the linear sequence of the antibody,for example, as catalogued by Kabat (Kabat et al., in “Sequences ofProteins of Immunological Interest,” 5^(th) Edition, U.S. Department ofHeath and Human Services, 1992). The Kabat numbering scheme is a widelyadopted standard for numbering the amino acid residues of an antibodyvariable domain in a consistent manner. Additional structuralconsiderations can also be used to determine the canonical structure ofan antibody. For example, those differences not fully reflected by Kabatnumbering can be described by the numbering system of Chothia et al.and/or revealed by other techniques, for example, crystallography andtwo or three-dimensional computational modeling. Accordingly, a givenantibody sequence may be placed into a canonical class which allows for,among other things, identifying appropriate chassis sequences (e.g.,based on a desire to include a variety of canonical structures in alibrary). Kabat numbering of antibody amino acid sequences andstructural considerations as described by Chothia et al., and theirimplications for construing canonical aspects of antibody structure, aredescribed in the literature.

The terms “CDR”, and its plural “CDRs”, refer to a complementaritydetermining region (CDR) of which three make up the binding character ofa light chain variable region (CDRL1, CDRL2 and CDRL3) and three make upthe binding character of a heavy chain variable region (CDRH1, CDRH2 andCDRH3). CDRs contribute to the functional activity of an antibodymolecule and are separated by amino acid sequences that comprisescaffolding or framework regions. The exact definitional CDR boundariesand lengths are subject to different classification and numberingsystems. CDRs may therefore be referred to by Kabat, Chothia, contact orany other boundary definitions, including the numbering system describedherein. Despite differing boundaries, each of these systems has somedegree of overlap in what constitutes the so called “hypervariableregions” within the variable sequences. CDR definitions according tothese systems may therefore differ in length and boundary areas withrespect to the adjacent framework region. See for example Kabat,Chothia, and/or MacCallum et al., (Kabat et al., in “Sequences ofProteins of Immunological Interest,” 5^(th) Edition, U.S. Department ofHealth and Human Services, 1992; Chothia et al., J. Mol. Biol., 1987,196: 901; and MacCallum et al., J. Mol. Biol., 1996, 262: 732, each ofwhich is incorporated by reference in its entirety).

The term “amino acid” or “amino acid residue” typically refers to anamino acid having its art recognized definition such as an amino acidselected from the group consisting of: alanine (Ala or A); arginine (Argor R); asparagine (Asn or N); aspartic acid (Asp or D); cysteine (Cys orC); glutamine (Gln or Q); glutamic acid (Glu or E); glycine (Gly or G);histidine (H is or H); isoleucine (Ile or I): leucine (Leu or L); lysine(Lys or K); methionine (Met or M); phenylalanine (Phe or F); proline(Pro or P); serine (Ser or S); threonine (Thr or T); tryptophan (Trp orW); tyrosine (Tyr or Y); and valine (Val or V), although modified,synthetic, or rare amino acids may be used as desired. Generally, aminoacids can be grouped as having a nonpolar side chain (e.g., Ala, Cys,Ile, Leu, Met, Phe, Pro, Val); a negatively charged side chain (e.g.,Asp, Glu); a positively charged sidechain (e.g., Arg, His, Lys); or anuncharged polar side chain (e.g., Asn, Cys, Gln, Gly, His, Met, Phe,Ser, Thr, Trp, and Tyr).

The term “polynucleotide(s)” refers to nucleic acids such as DNAmolecules and RNA molecules and analogs thereof (e.g., DNA or RNAgenerated using nucleotide analogs or using nucleic acid chemistry). Asdesired, the polynucleotides may be made synthetically, e.g., usingart-recognized nucleic acid chemistry or enzymatically using, e.g., apolymerase, and, if desired, be modified. Typical modifications includemethylation, biotinylation, and other art-known modifications. Inaddition, the nucleic acid molecule can be single-stranded ordouble-stranded and, where desired, linked to a detectable moiety.

The terms “theoretical diversity”, “theoretical total diversity”, or“theoretical repertoire” refer to the maximum number of variants in alibrary design. For example, given an amino acid sequence of threeresidues, where residues one and three may each be any one of five aminoacid types and residue two may be any one of 20 amino acid types, thetheoretical diversity is 5×20×5=500 possible sequences. Similarly ifsequence X is constructed by combination of 4 amino acid segments, wheresegment 1 has 100 possible sequences, segment 2 has 75 possiblesequences, segment 3 has 250 possible sequences, and segment 4 has 30possible sequences, the theoretical total diversity of fragment X wouldbe 100×75×200×30, or 5.6×10⁵ possible sequences.

The term “physical realization” refers to a portion of the theoreticaldiversity that can actually be physically sampled, for example, by anydisplay methodology. Exemplary display methodology include: phagedisplay, ribosomal display, and yeast display. For synthetic sequences,the size of the physical realization of a library depends on (1) thefraction of the theoretical diversity that can actually be synthesized,and (2) the limitations of the particular screening method. Exemplarylimitations of screening methods include the number of variants that canbe screened in a particular assay (e.g., ribosome display, phagedisplay, yeast display) and the transformation efficiency of a host cell(e.g., yeast, mammalian cells, bacteria) which is used in a screeningassay. For the purposes of illustration, given a library with atheoretical diversity of 10¹² members, an exemplary physical realizationof the library (e.g., in yeast, bacterial cells, ribosome display, etc.;details provided below) that can maximally include 10¹¹ members will,therefore, sample about 10% of the theoretical diversity of the library.However, if less than 10¹¹ members of the library with a theoreticaldiversity of 10¹² are synthesized, and the physical realization of thelibrary can maximally include 10¹¹ members, less than 10% of thetheoretical diversity of the library is sampled in the physicalrealization of the library. Similarly, a physical realization of thelibrary that can maximally include more than 10¹² members would“oversample” the theoretical diversity, meaning that each member may bepresent more than once (assuming that the entire 10¹² theoreticaldiversity is synthesized).

The term “all possible reading frames” encompasses at least the threeforward reading frames and, in some embodiments, the three reversereading frames.

The term “antibody of interest” refers to any antibody that has aproperty of interest that is isolated from a library of the invention.The property of interest may include, but is not limited to, binding toa particular antigen or epitope, blocking a binding interaction betweentwo molecules, or eliciting a certain biological effect.

The term “functionally expressed” refers to those immunoglobulin genesthat are expressed by human B cells and that do not contain prematurestop codons.

The term “full-length heavy chain” refers to an immunoglobulin heavychain that contains each of the canonical structural domains of animmunoglobulin heavy chain, including the four framework regions, thethree CDRs, and the constant region. The term “full-length light chain”refers to an immunoglobulin light chain that contains each of thecanonical structural domains of an immunoglobulin light chain, includingthe four framework regions, the three CDRs, and the constant region.

The term “unique,” as used herein, refers to a sequence that isdifferent (e.g. has a different chemical structure) from every othersequence within the designed theoretical diversity. It should beunderstood that there are likely to be more than one copy of many uniquesequences from the theoretical diversity in a particular physicalrealization. For example, a library comprising three unique sequencesmay comprise nine total members if each sequence occurs three times inthe library. However, in certain embodiments, each unique sequence mayoccur only once.

The term “heterologous moiety” is used herein to indicate the additionof a composition to an antibody wherein the composition is not normallypart of the antibody. Exemplary heterologous moieties include drugs,toxins, imaging agents, and any other compositions which might providean activity that is not inherent in the antibody itself.

As used herein, the term “percent occurrence of each amino acid residueat each position” refers to the percentage of instances in a sample inwhich an amino acid is found at a defined position within a particularsequence. For example, given the following three sequences:

-   -   K V R    -   K Y P    -   K R P,        K occurs in position one in 100% of the instances and P occurs        in position three in about 67% of the instances. In certain        embodiments of the invention, the sequences selected for        comparison are human immunoglobulin sequences.

As used herein, the term “most frequently occurring amino acids” at aspecified position of a sequence in a population of polypeptides refersto the amino acid residues that have the highest percent occurrence atthe indicated position in the indicated polypeptide population. Forexample, the most frequently occurring amino acids in each of the threemost N-terminal positions in N1 sequences of CDRH3 sequences that arefunctionally expressed by human B cells are listed in Table 21, and themost frequently occurring amino acids in each of the three mostN-terminal positions in N2 sequences of CDRH3 sequences that arefunctionally expressed by human B cells are listed in Table 22.

For the purposes of analyzing the occurrence of certain duplets (Example13) and the information content (Example 14) of the libraries of theinvention, and other libraries, a “central loop” of CDRH3 is defined. Ifthe C-terminal 5 amino acids from Kabat CDRH3 (95-102) are removed, thenthe remaining sequence is termed the “central loop”. Thus, consideringthe duplet occurrence calculations of Example 13, using a CDRH3 of size6 or less would not contribute to the analysis of the occurrence ofduplets. A CDRH3 of size 7 would contribute only to the i-i+1 data set,a CDRH3 of size 8 would also contribute to the i-i+2 data set, and aCDRH3 of size 9 and larger would also contribute to the i-i+3 data set.For example, a CDR H3 of size 9 may have amino acids at positions95-96-97-98-99-100-100A-101-102, but only the first four residues(bolded) would be part of the central loop and contribute to thepair-wise occurrence (duplet) statistics. As a further example, a CDRH3of size 14 may have the sequence:95-96-97-98-99-100-100A-100B-100C-100D-100E-100E-101-102. Here, only thefirst nine residues (bolded) contribute to the central loop.

Library screening requires a genotype-phenotype linkage. The term“genotype-phenotype linkage” is used in a manner consistent with itsart-recognized meaning and refers to the fact that the nucleic acid(genotype) encoding a protein with a particular phenotype (e.g., bindingan antigen) can be isolated from a library. For the purposes ofillustration, an antibody fragment expressed on the surface of a phagecan be isolated based on its binding to an antigen (e.g., Ladner etal.). The binding of the antibody to the antigen simultaneously enablesthe isolation of the phage containing the nucleic acid encoding theantibody fragment. Thus, the phenotype (antigen-binding characteristicsof the antibody fragment) has been “linked” to the genotype (nucleicacid encoding the antibody fragment). Other methods of maintaining agenotype-phenotype linkage include those of Wittrup et al. (U.S. Pat.Nos. 6,300,065, 6,331,391, 6,423,538, 6,696,251, 6,699,658, and US Pub.No. 20040146976, each of which is incorporated by reference in itsentirety), Miltenyi (U.S. Pat. No. 7,166,423, incorporated by referencein its entirety), Fandl (U.S. Pat. No. 6,919,183, US Pub No.20060234311, each incorporated by reference in its entirety),Clausell-Tormos et al. (Chem. Biol., 2008, 15: 427, incorporated byreference in its entirety), Love et al. (Nat. Biotechnol., 2006, 24:703, incorporated by reference in its entirety), and Kelly et al. (Chem.Commun., 2007, 14: 1773, incorporated by reference in its entirety). Anymethod which localizes the antibody protein with the gene encoding theantibody, in a way in which they can both be recovered while the linkagebetween them is maintained, is suitable.

2. DESIGN OF THE LIBRARIES

The antibody libraries of the invention are designed to reflect certainaspects of the preimmune repertoire as naturally created by the humanimmune system. Certain libraries of the invention are based on rationaldesign informed by the collection of human V, D, and J genes, and otherlarge databases of human heavy and light chain sequences (e.g., publiclyknown germline sequences; sequences from Jackson et al., J. Immunol.Methods, 2007, 324: 26, incorporated by reference in its entirety;sequences from Lee et al., Immunogenetics, 2006, 57: 917, incorporatedby reference in its entirety; and sequences compiled for rearranged VKand Vλ—see Appendices A and B filed herewith). Additional informationmay be found, for example, in Scaviner et al., Exp. Clin. Immunogenet.,1999, 16: 234; Tomlinson et al., J. Mol. Biol., 1992, 227: 799; andMatsuda et al., J. Exp. Med., 1998, 188: 2151 each incorporated byreference in its entirety. In certain embodiments of the invention,cassettes representing the possible V, D, and J diversity found in thehuman repertoire, as well as junctional diversity (i.e., N1 and N2), aresynthesized de novo as single or double-stranded DNA oligonucleotides.In certain embodiments of the invention, oligonucleotide cassettesencoding CDR sequences are introduced into yeast along with one or moreacceptor vectors containing heavy or light chain chassis sequences. Noprimer-based PCR amplification or template-directed cloning steps frommammalian cDNA or mRNA are employed. Through standard homologousrecombination, the recipient yeast recombines the cassettes (e.g.,CDR3s) with the acceptor vector(s) containing the chassis sequence(s)and constant regions, to create a properly ordered synthetic,full-length human heavy chain and/or light chain immunoglobulin librarythat can be genetically propagated, expressed, displayed, and screened.One of ordinary skill in the art will readily recognize that the chassiscontained in the acceptor vector can be designed so as to produceconstructs other than full-length human heavy chains and/or lightchains. For example, in certain embodiments of the invention, thechassis may be designed to encode portions of a polypeptide encoding anantibody fragment or subunit of an antibody fragment, so that a sequenceencoding an antibody fragment, or subunit thereof, is produced when theoligonucleotide cassette containing the CDR is recombined with theacceptor vector.

In certain embodiments, the invention provides a synthetic, preimmunehuman antibody repertoire comprising about 10⁷ to about 10²⁰ antibodymembers, wherein the repertoire comprises:

(a) selected human antibody heavy chain chassis (i.e., amino acids 1 to94 of the heavy chain variable region, using Kabat's definition);

(b) a CDRH3 repertoire, designed based on the human IGHD and IGHJgermline sequences, the CDRH3 repertoire comprising the following:

-   -   (i) optionally, one or more tail regions;    -   (ii) one or more N1 regions, comprising about 0 to about 10        amino acids selected from the group consisting of fewer than 20        of the amino acid types preferentially encoded by the action of        terminal deoxynucleotidyl transferase (TdT) and functionally        expressed by human B cells;    -   (iii) one or DH segments, based on one or more selected IGHD        segments, and one or more N- or C-terminal truncations thereof;    -   (iv) one or more N2 regions, comprising about 0 to about 10        amino acids selected from the group consisting of fewer than 20        of the amino acids preferentially encoded by the activity of TdT        and functionally expressed by human B cells; and    -   (v) one or more H3-JH segments, based on one or more IGHJ        segments, and one or more N-terminal truncations thereof (e.g.,        down to XXWG);

(c) one or more selected human antibody kappa and/or lambda light chainchassis; and

(d) a CDRL3 repertoire designed based on the human IGLV and IGLJgermline sequences, wherein “L” may be a kappa or lambda light chain.

The heavy chain chassis may be any sequence with homology to Kabatresidues 1 to 94 of an immunoglobulin heavy chain variable domain.Non-limiting examples of heavy chain chassis are included in theExamples, and one of ordinary skill in the art will readily recognizethat the principles presented therein, and throughout the specification,may be used to derive additional heavy chain chassis.

As described above, the heavy chain chassis region is followed,optionally, by a “tail” region. The tail region comprises zero, one, ormore amino acids that may or may not be selected on the basis ofcomparing naturally occurring heavy chain sequences. For example, incertain embodiments of the invention, heavy chain sequences available inthe art may be compared, and the residues occurring most frequently inthe tail position in the naturally occurring sequences included in thelibrary (e.g., to produce sequences that most closely resemble humansequences). In other embodiments, amino acids that are used lessfrequently may be used. In still other embodiments, amino acids selectedfrom any group of amino acids may be used. In certain embodiments of theinvention, the length of the tail is zero (no residue) or one (e.g.,G/D/E) amino acid. For the purposes of clarity, and without being boundby theory, in the naturally occurring human repertoire, the first ⅔ ofthe codon encoding the tail residue is provided by the FRM3 region ofthe VH gene. The amino acid at this position in naturally occurringheavy chain sequences may thus be considered to be partially encoded bythe IGHV gene (⅔) and partially encoded by the CDRH3 (⅓). However, forthe purposes of clearly illustrating certain aspects of the invention,the entire codon encoding the tail residue (and, therefore, the aminoacid derived from it) is described herein as being part of the CDRH3sequence.

As described above, there are two peptide segments derived fromnucleotides which are added by TdT in the naturally occurring humanantibody repertoire. These segments are designated N1 and N2 (referredto herein as N1 and N2 segments, domains, regions or sequences). Incertain embodiments of the invention, N1 and N2 are about 0, 1, 2, or 3amino acids in length. Without being bound by theory, it is thought thatthese lengths most closely mimic the N1 and N2 lengths found in thehuman repertoire (see FIG. 2). In other embodiments of the invention, N1and N2 may be about 4, 5, 6, 7, 8, 9, or 10 amino acids in length.Similarly, the composition of the amino acid residues utilized toproduce the N1 and N2 segments may also vary. In certain embodiments ofthe invention, the amino acids used to produce N1 and N2 segments may beselected from amongst the eight most frequently occurring amino acids inthe N1 and N2 domains of the human repertoire (e.g., G, R, S, P, L, A,V, and T). In other embodiments of the invention, the amino acids usedto produce the N1 and N2 segments may be selected from the groupconsisting of fewer than about 20, 19, 18, 17, 16, 15, 14, 13, 12, 11,10, 9, 8, 7, 6, 5, 4, or 3 of the amino acids preferentially encoded bythe activity of TdT and functionally expressed by human B cells.Alternatively, N1 and N2 may comprise amino acids selected from anygroup of amino acids. It is not required that N1 and N2 be of a similarlength or composition, and independent variation of the length andcomposition of N1 and N2 is one method by which additional diversity maybe introduced into the library.

The DH segments of the libraries are based on the peptides encoded bythe naturally occurring IGHD gene repertoire, with progressive deletionof residues at the N- and C-termini IGHD genes may be read in multiplereading frames, and peptides representing these reading frames, andtheir N- and C-terminal deletions are also included in the libraries ofthe invention. In certain embodiments of the invention, DH segments asshort as three amino acid residues may be included in the libraries. Inother embodiments of the invention, DH segments as short as about 1, 2,4, 5, 6, 7, or 8 amino acids may be included in the libraries.

The H3-JH segments of the libraries are based on the peptides encoded bythe naturally occurring IGHJ gene repertoire, with progressive deletionof residues at the N-terminus. The N-terminal portion of the IGHJsegment that makes up part of the CDRH3 is referred to herein as H3-JH.In certain embodiments of the invention, the H3-JH segment may berepresented by progressive N-terminal deletions of one or more H3-JHresidues, down to two H3-JH residues. In other embodiments of theinvention, the H3-JH segments of the library may contain N-terminaldeletions (or no deletions) down to about 6, 5, 4, 3, 2, 1, or 0 H3-JHresidues.

The light chain chassis of the libraries may be any sequence withhomology to Kabat residues 1 to 88 of naturally occurring light chain (Kor 2) sequences. In certain embodiments of the invention, the lightchain chassis of the invention are synthesized in combinatorial fashion,utilizing VL and JL segments, to produce one or more libraries of lightchain sequences with diversity in the chassis and CDR3 sequences. Inother embodiments of the invention, the light chain CDR3 sequences aresynthesized using degenerate oligonucleotides or trinucleotides andrecombined with the light chain chassis and light chain constant region,to form full-length light chains.

The instant invention also provides methods for producing and using suchlibraries, as well as libraries comprising one or more immunoglobulindomains or antibody fragments. Design and synthesis of each component ofthe claimed antibody libraries is provided in more detail below.

2.1. Design of the Antibody Library Chassis Sequences

One step in building certain libraries of the invention is the selectionof chassis sequences, which are based on naturally occurring variabledomain sequences (e.g., IGHV and IGLV). This selection can be donearbitrarily, or by the selection of chassis that meet certain criteria.For example, the Kabat database, an electronic database containingnon-redundant rearranged antibody sequences, can be queried for thoseheavy and light chain germline sequences that are most frequentlyrepresented. The BLAST search algorithm, or more specialized tools suchas SoDA (Volpe et al., Bioinformatics, 2006, 22: 438-44, incorporated byreference in its entirety), can be used to compare rearranged antibodysequences with germline sequences, using the V BASE2 database (Retter etal., Nucleic Acids Res., 2005, 33: D671-D674), or similar collections ofhuman V, D, and J genes, to identify the germline families that are mostfrequently used to generate functional antibodies.

Several criteria can be utilized for the selection of chassis forinclusion in the libraries of the invention. For example, sequences thatare known (or have been determined) to express poorly in yeast, or otherorganisms used in the invention (e.g., bacteria, mammalian cells, fungi,or plants) can be excluded from the libraries. Chassis may also bechosen based on their representation in the peripheral blood of humans.In certain embodiments of the invention, it may be desirable to selectchassis that correspond to germline sequences that are highlyrepresented in the peripheral blood of humans. In other embodiments, itmay be desirable to select chassis that correspond to germline sequencesthat are less frequently represented, for example, to increase thecanonical diversity of the library. Therefore, chassis may be selectedto produce libraries that represent the largest and most structurallydiverse group of functional human antibodies. In other embodiments ofthe invention, less diverse chassis may be utilized, for example, if itis desirable to produce a smaller, more focused library with lesschassis variability and greater CDR variability. In some embodiments ofthe invention, chassis may be selected based on both their expression ina cell of the invention (e.g., a yeast cell) and the diversity ofcanonical structures represented by the selected sequences. One maytherefore produce a library with a diversity of canonical structuresthat express well in a cell of the invention.

2.1.1. Design of the Heavy Chain Chassis Sequences

In certain embodiments of the invention, the antibody library comprisesvariable heavy domains and variable light domains, or portions thereof.Each of these domains is built from certain components, which will bemore fully described in the examples provided herein. In certainembodiments, the libraries described herein may be used to isolate fullyhuman antibodies that can be used as diagnostics and/or therapeutics.Without being bound by theory, antibodies with sequences most similar oridentical to those most frequently found in peripheral blood (forexample, in humans) may be less likely to be immunogenic whenadministered as therapeutic agents.

Without being bound by theory, and for the purposes of illustratingcertain embodiments of the invention, the VH domains of the library maybe considered to comprise three primary components: (1) a VH “chassis”,which includes amino acids 1 to 94 (using Kabat numbering), (2) theCDRH3, which is defined herein to include the Kabat CDRH3 proper(positions 95-102), and (3) the FRM4 region, including amino acids 103to 113 (Kabat numbering). The overall VH structure may therefore bedepicted schematically (not to scale) as:

The selection and design of VH chassis sequences based on the human IGHVgermline repertoire will become more apparent upon review of theexamples provided herein. In certain embodiments of the invention, theVH chassis sequences selected for use in the library may correspond toall functionally expressed human IGHV germline sequences. Alternatively,IGHV germline sequences may be selected for representation in a libraryaccording to one or more criteria. For example, in certain embodimentsof the invention, the selected IGHV germline sequences may be amongthose that are most highly represented among antibody molecules isolatedfrom the peripheral blood of healthy adults, children, or fetuses.

In certain embodiments, it may be desirable to base the design of the VHchassis on the utilization of IGHV germline sequences in adults,children, or fetuses with a disease, for example, an autoimmune disease.Without being bound by theory, it is possible that analysis of germlinesequence usage in the antibody molecules isolated from the peripheralblood of individuals with autoimmune disease may provide informationuseful for the design of antibodies recognizing human antigens.

In some embodiments, the selection of IGHV germline sequences forrepresentation in a library of the invention may be based on theirfrequency of occurrence in the peripheral blood. For the purposes ofillustration, four IGHV1 germline sequences (IGHV1-2 (SEQ ID NO: 24),IGHV1-18 (SEQ ID NO: 25), IGHV1-46 (SEQ ID NO: 26), and IGHV1-69 (SEQ IDNO: 27)) comprise about 80% of the IGHV1 family repertoire in peripheralblood. Thus, the specific IGHV1 germline sequences selected forrepresentation in the library may include those that are most frequentlyoccurring and that cumulatively comprise at least about 80% of the IGHV1family repertoire found in peripheral blood. An analogous approach canbe used to select specific IGHV germline sequences from any other IGHVfamily (i.e., IGHV1, IGHV2, IGHV3, IGHV4, IGHV5, IGHV6, and IGHV7). Thespecific germline sequences chosen for representation of a particularIGHV family in a library of the invention may therefore comprise atleast about 100%, 99%, 98%, 97%, 96% 95%, 94%, 93%, 92%, 91% 90%, 89%,88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 75%, 70%, 65%, 60%, 55%,50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 0% of the particularIGHV family member repertoire found in peripheral blood.

In some embodiments, the selected IGHV germline sequences may be chosento maximize the structural diversity of the VH chassis library.Structural diversity may be evaluated by, for example, comparing thelengths, compositions, and canonical structures of CDRH1 and CDRH2 inthe IGHV germline sequences. In human IGHV sequences, the CDRH1 (Kabatdefinition) may have a length of 5, 6 or 7 amino acids, while CDRH2(Kabat definition) may have length of 16, 17, 18 or 19 amino acids. Theamino acid compositions of the IGHV germline sequences and, inparticular, the CDR domains, may be evaluated by sequence alignments, aspresented in the Examples. Canonical structure may be assigned, forexample, according to the methods described by Chothia et al., J. Mol.Biol., 1992, 227: 799, incorporated by reference in its entirety.

In certain embodiments of the invention, it may be advantageous todesign VH chassis based on IGHV germline sequences that may maximize theprobability of isolating an antibody with particular characteristics.For example, without being bound by theory, in some embodiments it maybe advantageous to restrict the IGHV germline sequences to include onlythose germline sequences that are utilized in antibodies undergoingclinical development, or antibodies that have been approved astherapeutics. On the other hand, in some embodiments, it may beadvantageous to produce libraries containing VH chassis that are notrepresented amongst clinically utilized antibodies. Such libraries maybe capable of yielding antibodies with novel properties that areadvantageous over those obtained with the use of “typical” IGHV germlinesequences, or enabling studies of the structures and properties of“atypical” IGHV germline sequences or canonical structures.

One of ordinary skill in the art will readily recognize that a varietyof other criteria can be used to select IGHV germline sequences forrepresentation in a library of the invention. Any of the criteriadescribed herein may also be combined with any other criteria. Furtherexemplary criteria include the ability to be expressed at sufficientlevels in certain cell culture systems, solubility in particularantibody formats (e.g., whole immunoglobulins and antibody fragments),and the thermodynamic stability of the individual domains, wholeimmunoglobulins, or antibody fragments. The methods of the invention maybe applied to select any IGHV germline sequence that has utility in anantibody library of the instant invention.

In certain embodiments of the invention, the VH chassis of the librariesmay comprise from about Kabat residue 1 to about Kabat residue 94 of oneor more of the following IGHV germline sequences: IGHV1-2 (SEQ ID NO:24), IGHV1-3 (SEQ ID NO: 423), IGHV1-8 (SEQ ID NO: 424, 425), IGHV1-18(SEQ ID NO: 25), IGHV1-24 (SEQ ID NO: 426), IGHV1-45 (SEQ ID NO: 427),IGHV1-46 (SEQ ID NO: 26), IGHV1-58 (SEQ ID NO: 428), IGHV1-69 (SEQ IDNO: 27), IGHV1-5 (SEQ ID NO: 429), IGHV1-26 (SEQ ID NO: 430), IGHV1-70(SEQ ID NO: 431, 432), IGHV3-7 (SEQ ID NO: 28), IGHV3-9 (SEQ ID NO:433), IGHV3-11 (SEQ ID NO: 434), IGHV3-13 (SEQ ID NO: 435), IGHV3-15(SEQ ID NO: 29), IGHV3-20 (SEQ ID NO: 436), IGHV3-21 (SEQ ID NO: 437),IGHV3-23 (SEQ ID NO: 30), IGHV3-30 (SEQ ID NO: 31), IGHV3-33 (SEQ ID NO:32), IGHV3-43 (SEQ ID NO: 438), IGHV3-48 (SEQ ID NO: 33), IGHV3-49 (SEQID NO: 439), IGHV3-53 (SEQ ID NO: 440), IGHV3-64 (SEQ ID NO: 441),IGHV3-66 (SEQ ID NO: 442), IGHV3-72 (SEQ ID NO: 443), IGHV3-73 (SEQ IDNO: 444), IGHV3-74 (SEQ ID NO: 445), IGHV4-4 (SEQ ID NO: 446, 447),IGHV4-28 (SEQ ID NO: 448), IGHV4-31 (SEQ ID NO: 34), IGHV4-34 (SEQ IDNO: 35), IGHV4-39 (SEQ ID NO: 36), IGHV4-59 (SEQ ID NO: 37), IGHV4-61(SEQ ID NO: 38), IGHV4-B (SEQ ID NO: 39), IGHV5-51 (SEQ ID NO: 40),IGHV6-1 (SEQ ID NO: 449), and IGHV7-4-1 (SEQ ID NO: 450). In someembodiments of the invention, a library may contain one or more of thesesequences, one or more allelic variants of these sequences, or encode anamino acid sequence at least about 99.9%, 99.5%, 99%, 98.5%, 98%, 97.5%,97%, 96.5%, 96%, 95.5%, 95%, 94.5%, 94%, 93.5%, 93%, 92.5%, 92%, 91.5%,91%, 90.5%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%,77.5%, 75%, 73.5%, 70%, 65%, 60%, 55%, or 50% identical to one or moreof these sequences.

In other embodiments, the VH chassis of the libraries may comprise fromabout Kabat residue 1 to about Kabat residue 94 of the following IGHVgermline sequences: IGHV1-2 (SEQ ID NO: 24), IGHV1-18 (SEQ ID NO: 25),IGHV1-46 (SEQ ID NO: 26), IGHV1-69 (SEQ ID NO: 27), IGHV3-7 (SEQ ID NO:28), IGHV3-15 (SEQ ID NO: 29), IGHV3-23 (SEQ ID NO: 30), IGHV3-30 (SEQID NO: 31), IGHV3-33 (SEQ ID NO: 32), IGHV3-48 (SEQ ID NO: 33), IGHV4-31(SEQ ID NO: 34), IGHV4-34 (SEQ ID NO: 35), IGHV4-39 (SEQ ID NO: 36),IGHV4-59 (SEQ ID NO: 37), IGHV4-61 (SEQ ID NO: 38), IGHV4-B (SEQ ID NO:39), and IGHV5-51 (SEQ ID NO: 40). In some embodiments of the invention,a library may contain one or more of these sequences, one or moreallelic variants of these sequences, or encode an amino acid sequence atleast about 99.9%, 99.5%, 99%, 98.5%, 98%, 97.5%, 97%, 96.5%, 96%,95.5%, 95%, 94.5%, 94%, 93.5%, 93%, 92.5%, 92%, 91.5%, 91%, 90.5%, 90%,89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 77.5%, 75%, 73.5%,70%, 65%, 60%, 55%, or 50% identical to one or more of these sequences.The amino acid sequences of these chassis are presented in Table 5.

2.1.1.1. Heavy Chain Chassis Variants

While the selection of the VH chassis with sequences based on the IGHVgermline sequences is expected to support a large diversity of CDRH3sequences, further diversity in the VH chassis may be generated byaltering the amino acid residues comprising the CDRH1 and/or CDRH2regions of each chassis selected for inclusion in the library (seeExample 2).

In certain embodiments of the invention, the alterations or mutations inthe amino acid residues comprising the CDRH1 and CDRH2 regions, or otherregions, of the IGHV germline sequences are made after analyzing thesequence identity within data sets of rearranged human heavy chainsequences that have been classified according to the identity of theoriginal IGHV germline sequence from which the rearranged sequences arederived. For example, from a set of rearranged antibody sequences, theIGHV germline sequence of each antibody is determined, and therearranged sequences are classified according to the IGHV germlinesequence. This determination is made on the basis of sequence identity.

Next, the occurrence of any of the 20 amino acid residues at eachposition in these sequences is determined. In certain embodiments of theinvention, one may be particularly interested in the occurrence ofdifferent amino acid residues at the positions within CDRH1 and CDRH2,for example if increasing the diversity of the antigen-binding portionof the VH chassis is desired. In other embodiments of the invention, itmay be desirable to evaluate the occurrence of different amino acidresidues in the framework regions. Without being bound by theory,alterations in the framework regions may impact antigen binding byaltering the spatial orientation of the CDRs.

After the occurrence of amino acids at each position of interest hasbeen identified, alterations may be made in the VH chassis sequence,according to certain criteria. In some embodiments, the objective may beto produce additional VH chassis with sequence variability that mimicsthe variability observed in the heavy chain domains of rearranged humanantibody sequences (derived from respective IGHV germline sequences) asclosely as possible, thereby potentially obtaining sequences that aremost human in nature (i.e., sequences that most closely mimic thecomposition and length of human sequences). In this case, one maysynthesize additional VH chassis sequences that include mutationsnaturally found at a particular position and include one or more ofthese VH chassis sequences in a library of the invention, for example,at a frequency that mimics the frequency found in nature. In anotherembodiment of the invention, one may wish to include VH chassis thatrepresent only mutations that most frequently occur at a given positionin rearranged human antibody sequences. For example, rather thanmimicking the human variability precisely, as described above, and withreference to exemplary Tables 6 and 7, one may choose to include onlytop 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or1, amino acid residues that most frequently occur at each position. Forthe purposes of illustration, and with reference to Table 6, if onewished to include the top four most frequently occurring amino acidresidues at position 31 of the VH1-69 sequence, then position 31 in theVH1-69 sequence would be varied to include S, N, T, and R. Without beingbound by theory, it is thought that the introduction of diversity bymimicking the naturally occurring composition of the rearranged heavychain sequences is likely to produce antibodies that are most human incomposition. However, the libraries of the invention are not limited toheavy chain sequences that are diversified by this method, and anycriteria can be used to introduce diversity into the heavy chainchassis, including random or rational mutagenesis. For example, incertain embodiments of the invention, it may be preferable to substituteneutral and/or smaller amino acid residues for those residues that occurin the IGHV germline sequence. Without being bound by theory, neutraland/or smaller amino acid residues may provide a more flexible and lesssterically hindered context for the display of a diversity of CDRsequences.

Example 2 illustrates the application of this method to heavy chainsderived from a particular IGHV germline. One of ordinary skill in theart will readily recognize that this method can be applied to anygermline sequence, and can be used to generate at least about 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,1000, 10⁴, 10⁵, 10⁶, or more variants of each heavy chain chassis.

2.1.2. Design of the Light Chain Chassis Sequences

The light chain chassis of the invention may be based on kappa and/orlambda light chain sequences. The principles underlying the selection oflight chain variable (IGLV) germline sequences for representation in thelibrary are analogous to those employed for the selection of the heavychain sequences (described above and in Examples 1 and 2). Similarly,the methods used to introduce variability into the selected heavy chainchassis may also be used to introduce variability into the light chainchassis.

Without being bound by theory, and for the purposes of illustratingcertain embodiments of the invention, the VL domains of the library maybe considered to comprise three primary components: (1) a VL “chassis”,which includes amino acids 1 to 88 (using Kabat numbering), (2) theVLCDR3, which is defined herein to include the Kabat CDRL3 proper(positions 89-97), and (3) the FRM4 region, including amino acids 98 to107 (Kabat numbering). The overall VL structure may therefore bedepicted schematically (not to scale) as:

In certain embodiments of the invention, the VL chassis of the librariesinclude one or more chassis based on IGKV germline sequences. In certainembodiments of the invention, the VL chassis of the libraries maycomprise from about Kabat residue 1 to about Kabat residue 88 of one ormore of the following IGKV germline sequences: IGKV1-05 (SEQ ID NO:229), IGKV1-06 (SEQ ID NO: 451), IGKV1-08 (SEQ ID NO: 452, 453),IGKV1-09 (SEQ ID NO: 454), IGKV1-12 (SEQ ID NO: 230), IGKV1-13 (SEQ IDNO: 455), IGKV1-16 (SEQ ID NO: 456), IGKV1-17 (SEQ ID NO: 457), IGKV1-27(SEQ ID NO: 231), IGKV1-33 (SEQ ID NO: 232), IGKV1-37 (SEQ ID NOs: 458,459), IGKV1-39 (SEQ ID NO: 233), IGKV1D-16 (SEQ ID NO: 460), IGKV1D-17(SEQ ID NO: 461), IGKV1D-43 (SEQ ID NO: 462), IGKV1D-8 (SEQ ID NOs: 463,464), IGKV2-24 (SEQ ID NO: 465), IGKV2-28 (SEQ ID NO: 234), IGKV2-29(SEQ ID NO: 466), IGKV2-30 (SEQ ID NO: 467), IGKV2-40 (SEQ ID NO: 468),IGKV2D-26 (SEQ ID NO: 469), IGKV2D-29 (SEQ ID NO: 470), IGKV2D-30 (SEQID NO: 471), IGKV3-11 (SEQ ID NO: 235), IGKV3-15 (SEQ ID NO: 236),IGKV3-20 (SEQ ID NO: 237), IGKV3D-07 (SEQ ID NO: 472), IGKV3D-11 (SEQ IDNO: 473), IGKV3D-20 (SEQ ID NO: 474), IGKV4-1 (SEQ ID NO: 238), IGKV5-2(SEQ ID NOs: 475, 476), IGKV6-21 (SEQ ID NOs: 477), and IGKV6D-41. Insome embodiments of the invention, a library may contain one or more ofthese sequences, one or more allelic variants of these sequences, orencode an amino acid sequence at least about 99.9%, 99.5%, 99%, 98.5%,98%, 97.5%, 97%, 96.5%, 96%, 95.5%, 95%, 94.5%, 94%, 93.5%, 93%, 92.5%,92%, 91.5%, 91%, 90.5%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%,81%, 80%, 77.5%, 75%, 73.5%, 70%, 65%, 60%, 55%, or 50% identical to oneor more of these sequences.

In other embodiments, the VL chassis of the libraries may comprise fromabout Kabat residue 1 to about Kabat residue 88 of the following IGKVgermline sequences: IGKV1-05 (SEQ ID NO: 229), IGKV1-12 (SEQ ID NO:230), IGKV1-27 (SEQ ID NO: 231), IGKV1-33 (SEQ ID NO: 232), IGKV1-39(SEQ ID NO: 233), IGKV2-28 (SEQ ID NO: 234), IGKV3-11 (SEQ ID NO: 235),IGKV3-15 (SEQ ID NO: 236), IGKV3-20 (SEQ ID NO: 237), and IGKV4-1 (SEQID NO: 238). In some embodiments of the invention, a library may containone or more of these sequences, one or more allelic variants of thesesequences, or encode an amino acid sequence at least about 99.9%, 99.5%,99%, 98.5%, 98%, 97.5%, 97%, 96.5%, 96%, 95.5%, 95%, 94.5%, 94%, 93.5%,93%, 92.5%, 92%, 91.5%, 91%, 90.5%, 90%, 89%, 88%, 87%, 86%, 85%, 84%,83%, 82%, 81%, 80%, 77.5%, 75%, 73.5%, 70%, 65%, 60%, 55%, or 50%identical to one or more of these sequences. The amino acid sequences ofthese chassis are presented in Table 11.

In certain embodiments of the invention, the VL chassis of the librariesinclude one or more chassis based on IGλV germline sequences. In certainembodiments of the invention, the VL chassis of the libraries maycomprise from about Kabat residue 1 to about Kabat residue 88 of one ormore of the following IGλV germline sequences: IGλV3-1 (SEQ ID NO: 535),IGλV3-21 (SEQ ID NO: 537), IGλV2-14 (SEQ ID NO: 534), IGλV1-40 (SEQ IDNO: 531), IGλV3-19 (SEQ ID NO: 536), IGλV1-51 (SEQ ID NO: 533), IGλV1-44(SEQ ID NO: 532), IGλV6-57 (SEQ ID NO: 539), IGλV2-8, IGλV3-25,IGλV2-23, IGλV3-10, IGλV4-69 (SEQ ID NO: 538), IGλV1-47, IGλV2-11,IGλV7-43 (SEQ ID NO: 541), IGλV7-46, IGλV5-45 (SEQ ID NO: 540),IGλV4-60, IGλV10-54 (SEQ ID NO: 482), IGλV8-61 (SEQ ID NO: 499), IGλV3-9(SEQ ID NO: 494), IGλV1-36 (SEQ ID NO: 480), IGλV2-18 (SEQ ID NO: 485),IGλV3-16 (SEQ ID NO: 491), IGλV3-27 (SEQ ID NO: 493), IGλV4-3 (SEQ IDNO: 495), IGλV5-39 (SEQ ID NO: 497), IGλV9-49 (SEQ ID NO: 500), andIGλV3-12 (SEQ ID NO: 490). In some embodiments of the invention, alibrary may contain one or more of these sequences, one or more allelicvariants of these sequences, or encode an amino acid sequence at leastabout 99.9%, 99.5%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%,85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% identical to one or more ofthese sequences.

In other embodiments, the VL chassis of the libraries may comprise fromabout Kabat residue 1 to about Kabat residue 88 of the following IGλVgermline sequences: IGλV3-1 (SEQ ID NO: 535), IGλV3-21 (SEQ ID NO: 537),IGλV2-14 (SEQ ID NO: 534), IGλV1-40 (SEQ ID NO: 531), IGλV3-19 (SEQ IDNO: 536), IGλV1-51 (SEQ ID NO: 533), IGλV1-44 (SEQ ID NO: 532), IGλV6-57(SEQ ID NO: 539), IGλV4-69 (SEQ ID NO: 538), IGλV7-43 (SEQ ID NO: 541),and IGλV5-45 (SEQ ID NO: 540). In some embodiments of the invention, alibrary may contain one or more of these sequences, one or more allelicvariants of these sequences, or encode an amino acid sequence at leastabout 99.9%, 99.5%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%,85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% identical to one or more ofthese sequences. The amino acid sequences of these chassis are presentedin Table 14.

2.2. Design of the Antibody Library CDRH3 Components

It is known in the art that diversity in the CDR3 region of the heavychain is sufficient for most antibody specificities (Xu and Davis,Immunity, 2000, 13: 27-45, incorporated by reference in its entirety)and that existing successful libraries have been created using CDRH3 asthe major source of diversification (Hoogenboom et al., J. Mol. Biol.,1992, 227: 381; Lee et al., J. Mol. Biol., 2004, 340: 1073 each of whichis incorporated by reference in its entirety). It is also known thatboth the DH region and the N1/N2 regions contribute to the CDRH3functional diversity (Schroeder et al., J. Immunol., 2005, 174: 7773 andMathis et al., Eur J. Immunol., 1995, 25: 3115, each of which isincorporated by reference in its entirety). For the purposes of thepresent invention, the CDHR3 region of naturally occurring humanantibodies can be divided into five segments: (1) the tail segment, (2)the N1 segment, (3) the DH segment, (4) the N2 segment, and (5) the JHsegment. As exemplified below, the tail, N1 and N2 segments may or maynot be present.

In certain embodiments of the invention, the method for selecting aminoacid sequences for the synthetic CDRH3 libraries includes a frequencyanalysis and the generation of the corresponding variability profiles ofexisting rearranged antibody sequences. In this process, which isdescribed in more detail in the Examples section, the frequency ofoccurrence of a particular amino acid residue at a particular positionwithin rearranged CDRH3s (or any other heavy or light chain region) isdetermined Amino acids that are used more frequently in nature may thenbe chosen for inclusion in a library of the invention.

2.2.1. Design and Selection of the DH Segment Repertoire

In certain embodiments of the invention, the libraries contain CDRH3regions comprising one or more segments designed based on the IGHD genegermline repertoire. In some embodiments of the invention, DH segmentsselected for inclusion in the library are selected and designed based onthe most frequent usage of human IGHD genes, and progressive N-terminaland C-terminal deletions thereof, to mimic the in vivo processing of theIGHD gene segments. In some embodiments of the invention, the DHsegments of the library are about 3 to about 10 amino acids in length.In some embodiments of the invention, the DH segments of the library areabout 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids in length, or acombination thereof. In certain embodiments, the libraries of theinvention may contain DH segments with a wide distribution of lengths(e.g., about 0 to about 10 amino acids). In other embodiments, thelength distribution of the DH may be restricted (e.g., about 1 to about5 amino acids, about 3 amino acids, about 3 and about 5 amino acids, andso on). In certain embodiments of the library, the shortest DH segmentsmay be about 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids.

In certain embodiments of the invention, libraries may contain DHsegments representative of any reading frame of any IGHD germlinesequence. In certain embodiments of the invention, the DH segmentsselected for inclusion in a library include one or more of the followingIGHD sequences, or their derivatives (i.e., any reading frame and anydegree of N-terminal and C-terminal truncation): IGHD3-10 (SEQ ID NOs:1-3), IGHD3-22 (SEQ ID NOs: 239, 4, 240), IGHD6-19 (SEQ ID NOs: 5, 6,241), IGHD6-13 (SEQ ID NOs: 7, 8, 242), IGHD3-3 (SEQ ID NOs: 243, 244,9), IGHD2-2 (SEQ ID NOs: 245, 10, 11), IGHD4-17 (SEQ ID NOs: 246, 12,247), IGHD1-26 (SEQ ID NOs: 13, 248 and 14), IGHD5-5/5-18 (SEQ ID NOs:249, 250, 15), IGHD2-15 (SEQ ID NOs: 251, 16, 252), IGHD6-6 (encoded bySEQ ID NO: 515), IGHD3-9 (encoded by SEQ ID NO: 509), IGHD5-12 (encodedby SEQ ID NO: 512), IGHD5-24 (encoded by SEQ ID NO: 513), IGHD2-21(encoded by SEQ ID NOs: 505 and 506), IGHD3-16 (encoded by SEQ ID NO:508), IGHD4-23 (encoded by SEQ ID NO: 510), IGHD1-1 (encoded by SEQ IDNO: 501), IGHD1-7 (encoded by SEQ ID NO: 504), IGHD4-4/4-11 (encoded bySEQ ID NO: 511), IGHD1-20 (encoded by SEQ ID NO: 503), IGHD7-27,IGHD2-8, and IGHD6-25. In some embodiments of the invention, a librarymay contain one or more of these sequences, allelic variants thereof, orencode an amino acid sequence at least about 99.9%, 99.5%, 99%, 98.5%,98%, 97.5%, 97%, 96.5%, 96%, 95.5%, 95%, 94.5%, 94%, 93.5%, 93%, 92.5%,92%, 91.5%, 91%, 90.5%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%,81%, 80%, 77.5%, 75%, 73.5%, 70%, 65%, 60%, 55%, or 50% identical to oneor more of these sequences.

For the purposes of illustration, progressive N-terminal and C-terminaldeletions of IGHD3-10, reading frame 1, are enumerated in the Table 1.N-terminal and C-terminal deletions of other IGHD sequences and readingframes are also encompassed by the invention, and one of ordinary skillin the art can readily determine these sequences using, for example, thenon-limiting exemplary data presented in Table 16. and/or the methodsoutlined above. Table 18 (Example 5) enumerates certain DH segments usedin certain embodiments of the invention.

TABLE 1 Example of Progressive N- and   C-terminal Deletions of Reading Frame 1 for Gene IGHD3-10,  Yielding DH Segments DH SEQ ID NO: VLLWFGELL  1 VLLWFGEL 593 VLLWFGE 594 VLLLWFG 595 VLLWF 596 VLLW 597 VLL LLWFGELL598 LLWFGEL 599 LLWFGE 600 LLWFG 601 LLWF 602 LLW LWFGELL 603 LWFGEL 604LWFGE 605 LWFG 606 LWF WFGELL 607 WFGEL 608 WFGE 609 WFG FGELL 610 FGEL611 FGE GELL 612 GEL ELL

In certain embodiments of the invention, the DH segments selected forinclusion in a library include one or more of the following IGHDsequences, or their derivatives (i.e., any reading frame and any degreeN-terminal and C-terminal truncation): IGHD3-10 (SEQ ID NOs: 1-3),IGHD3-22 (SEQ ID NOs: 239, 4, 240), IGHD6-19 (SEQ ID NOs: 5, 6, 241),IGHD6-13 (SEQ ID NOs: 7, 8, 242), IGHD3-03 (SEQ ID NOs: 243, 244, 9),IGHD2-02 (SEQ ID NOs: 245, 10, 11), IGHD4-17 (SEQ ID NOs: 246, 12, 247),IGHD1-26 (SEQ ID NOs: 13, 248 and 14), IGHD5-5/5-18 (SEQ ID NOs: 249,250, 15), and IGHD2-15 (SEQ ID NOs: 251, 16, 252). In some embodimentsof the invention, a library may contain one or more of these sequences,allelic variants thereof, or encode an amino acid sequence at leastabout 99.9%, 99.5%, 99%, 98.5%, 98%, 97.5%, 97%, 96.5%, 96%, 95.5%, 95%,94.5%, 94%, 93.5%, 93%, 92.5%, 92%, 91.5%, 91%, 90.5%, 90%, 89%, 88%,87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 77.5%, 75%, 73.5%, 70%, 65%,60%, 55%, or 50% identical to one or more of these sequences.

In certain embodiments of the invention, the DH segments selected forinclusion in a library include one or more of the following IGHDsequences, wherein the notation “_x” denotes the reading frame of thegene, or their derivatives (i.e., any degree of N-terminal or C-terminaltruncation): IGHD1-26_(—)1 (SEQ ID NO: 13), IGHD1-26_(—)3 (SEQ ID NO:14), IGHD2-2_(—)2 (SEQ ID NO: 10), IGHD2-2_(—)3 (SEQ ID NO: 11),IGHD2-15_(—)2 (SEQ ID NO: 16), IGHD3-3_(—)3 (SEQ ID NO: 9),IGHD3-10_(—)1 (SEQ ID NO: 1), IGHD3-10_(—)2 (SEQ ID NO: 2),IGHD3-10_(—)3 (SEQ ID NO: 3), IGHD3-22_(—)2 (SEQ ID NO: 4),IGHD4-17_(—)2 (SEQ ID NO: 12), IGHD5-5_(—)3 (SEQ ID NO: 15),IGHD6-13_(—)1 (SEQ ID NO: 7), IGHD6-13_(—)2 (SEQ ID NO: 8),IGHD6-19_(—)1 (SEQ ID NO: 5), and IGHD6-19_(—)2 (SEQ ID NO: 6). In someembodiments of the invention, a library may contain one or more of thesesequences, allelic variants thereof, or encode an amino acid sequence atleast about 99.9%, 99.5%, 99%, 98.5%, 98%, 97.5%, 97%, 96.5%, 96%,95.5%, 95%, 94.5%, 94%, 93.5%, 93%, 92.5%, 92%, 91.5%, 91%, 90.5%, 90%,89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 77.5%, 75%, 73.5%,70%, 65%, 60%, 55%, or 50% identical to one or more of these sequences.

In certain embodiments of the invention, the libraries are designed toreflect a pre-determined length distribution of N- and C-terminaldeleted IGHD segments. For example, in certain embodiments of thelibrary, the DH segments of the library may be designed to mimic thenatural length distribution of DH segments found in the humanrepertoire. For example, the relative occurrence of different IGHDsegments in rearranged human antibody heavy chain domains from Lee etal. (Immunogenetics, 2006, 57: 917, incorporated by reference in itsentirety). Table 2 shows the relative occurrence of the top 68% of IGHDsegments from Lee et al.

TABLE 2 Relative Occurrence of Top 68% of IGHD Gene Usage from Lee et al. IGHD SEQ Reading Sequence IDRelative  Frame (Parent) NO: Occurrence IGHD3-10_1 VLLWFGELL  1  4.3%IGHD3-10_2 YYYGSGSYYN  2  8.4% IGHD3-10_3 ITMVRGVII  3  4.0% IGHD3-22_2YYYDSSGYYY  4 15.6% IGHD6-19_1 GYSSGWY  5  7.4% IGHD6-19_2 GIAVAG  6 6.0% IGHD6-13_1 GYSSSWY  7  8.4% IGHD6-13_2 GIAAAG  8  5.3% IGHD3-3_3ITIFGVVII  9  7.4% IGHD2-2_2 GYCSSTSCYT 10  5.2% IGHD2-2_3 DIVVVPAAM 11 4.1% IGHD4-17_2 DYGDY 12  6.8% IGHD1-26_1 GIVGATT 13  2.9% IGHD1-26_3YSGSYY 14  4.3% IGHD5-5_3 GYSYGY 15  4.3% IGHD2-15_2 GYCSGGSCYS 16  5.6%

In certain embodiments, these relative occurrences may be used to designa library with DH prevalence that is similar to the IGHD usage found inperipheral blood. In other embodiments of the invention, it may bepreferable to bias the library toward longer or shorter DH segments, orDH segments of a particular composition. In other embodiments, it may bedesirable to use all DH segments selected for the library in equalproportion.

In certain embodiments of the invention, the most commonly usedreading-frames of the ten most frequently occurring IGHD sequences areutilized, and progressive N-terminal and C-terminal deletions of thesesequences are made, thus providing a total of 278 non-redundant DHsegments that are used to create a CDRH3 repertoire of the instantinvention (Table 18). In some embodiments of the invention, the methodsdescribed above can be applied to produce libraries comprising the top1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, or 25 expressed IGHD sequences, and progressiveN-terminal and C-terminal deletions thereof. As with all othercomponents of the library, while the DH segments may be selected fromamong those that are commonly expressed, it is also within the scope ofthe invention to select these gene segments based on the fact that theyare less commonly expressed. This may be advantageous, for example, inobtaining antibodies toward self-antigens or in further expanding thediversity of the library. Alternatively, DH segments can be used to addcompositional diversity in a manner that is strictly relative to theiroccurrence in actual human heavy chain sequences.

In certain embodiments of the invention, the progressive deletion ofIGHD genes containing disulfide loop encoding segments may be limited,so as to leave the loop intact and to avoid the presence of unpairedcysteine residues. In other embodiments of the invention, the presenceof the loop can be ignored and the progressive deletion of the IGHD genesegments can occur as for any other segments, regardless of the presenceof unpaired cysteine residues. In still other embodiments of theinvention, the cysteine residues can be mutated to any other amino acid.

2.2.2. Design and Selection of the H3-JH Segment Repertoire

There are six IGHJ (joining) segments, IGHJ1 (SEQ ID NO: 253), IGHJ2(SEQ ID NO: 254), IGHJ3 (SEQ ID NO: 255), IGHJ4 (SEQ ID NO: 256), IGHJ5(SEQ ID NO: 257), and IGHJ6 (SEQ ID NO: 258). The amino acid sequencesof the parent segments and the progressive N-terminal deletions arepresented in Table 20 (Example 5). Similar to the N- and C-terminaldeletions that the IGHD genes undergo, natural variation is introducedinto the IGHJ genes by N-terminal “nibbling”, or progressive deletion,of one or more codons by exonuclease activity.

The H3-JH segment refers to the portion of the IGHJ segment that is partof CDRH3. In certain embodiments of the invention, the H3-JH segment ofa library comprises one or more of the following sequences: AEYFQH (SEQID NO: 17), EYFQH (SEQ ID NO: 583), YFQH (SEQ ID NO: 584), FQH, QH, H,YWYFDL (SEQ ID NO: 18), WYFDL (SEQ ID NO: 585), YFDL (SEQ ID NO: 586),FDL, DL, L, AFDV (SEQ ID NO: 19), FDV, DV, V, YFDY (SEQ ID NO: 20), FDY,DY, Y, NWFDS (SEQ ID NO: 21), WFDS (SEQ ID NO: 587), FDS, DS, S,YYYYYGMDV (SEQ ID NO: 22), YYYYGMDV (SEQ ID NO: 588), YYYGMDV (SEQ IDNO: 589), YYGMDV (SEQ ID NO: 590), YGMDV (SEQ ID NO: 591), GMDV (SEQ IDNO: 592), MDV, and DV. In some embodiments of the invention, a librarymay contain one or more of these sequences, allelic variations thereof,or encode an amino acid sequence at least about 99.9%, 99.5%, 99%,98.5%, 98%, 97.5%, 97%, 96.5%, 96%, 95.5%, 95%, 94.5%, 94%, 93.5%, 93%,92.5%, 92%, 91.5%, 91%, 90.5%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%,82%, 81%, 80%, 77.5%, 75%, 73.5%, 70%, 65%, 60%, 60%, 55%, or 50%identical to one or more of these sequences.

In other embodiments of the invention, the H3-JH segment may compriseabout 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or more amino acids. For example,the H3-JH segment of JH1_(—)4 (Table 20) has a length of three residues,while non-deleted JH6 has an H3-JH segment length of nine residues. TheFRM4-JH region of the IGHJ segment begins with the sequence WG(Q/R)G(SEQ ID NO: 23) and corresponds to the portion of the IGHJ segment thatmakes up part of framework 4. In certain embodiments of the invention,as enumerated in Table 20, there are 28 H3-JH segments that are includedin a library. In certain other embodiments, libraries may be produced byutilizing about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 of the IGHJsegments enumerated above or in Table 20.

2.2.3. Design and Selection of the N1 and N2 Segment Repertoires

Terminal deoxynucleotidyl transferase (TdT) is a highly conserved enzymefrom vertebrates that catalyzes the attachment of 5′ triphosphates tothe 3′ hydroxyl group of single- or double-stranded DNA. Hence, theenzyme acts as a template-independent polymerase (Koiwai et al., NucleicAcids Res., 1986, 14: 5777; Basu et al., Biochem. Biophys. Res. Comm.,1983, 111: 1105, each incorporated by reference in its entirety). Invivo, TdT is responsible for the addition of nucleotides to the V-D andD-J junctions of antibody heavy chains (Alt and Baltimore, PNAS, 1982,79: 4118; Collins et al., J. Immunol., 2004, 172: 340, each incorporatedby reference in its entirety). Specifically, TdT is responsible forcreating the N1 and N2 (non-templated) segments that flank the D(diversity) region.

In certain embodiments of the invention, the length and composition ofthe N1 and N2 segments are designed rationally, according to statisticalbiases in amino acid usage found in naturally occurring N1 and N2segments in human antibodies. One embodiment of a library produced viathis method is described in Example 5. According to data compiled fromhuman databases (Jackson et al., J. Immunol. Methods, 2007, 324: 26,incorporated by reference in its entirety), there are an average of 3.02amino acid insertions for N1 and 2.4 amino acid insertions for N2, nottaking into account insertions of two nucleotides or less (FIG. 2). Incertain embodiments of the invention, N1 and N2 segments are restrictedto lengths of zero to three amino acids. In other embodiments of theinvention, N1 and N2 may be restricted to lengths of less than about 4,5, 6, 7, 8, 9, or 10 amino acids.

In some embodiments of the invention, the composition of these sequencesmay be chosen according to the frequency of occurrence of particularamino acids in the N1 and N2 sequences of natural human antibodies (forexamples of this analysis, see, Tables 21 to 23, in Example 5). Incertain embodiments of the invention, the eight most commonly occurringamino acids in these regions (i.e., G, R, S, P, L, A, T, and V) are usedto design the synthetic N1 and N2 segments. In other embodiments of theinvention about the most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, or 19 most commonly occurring amino acids may be used inthe design of the synthetic N1 and N2 segments. In still otherembodiments, all 20 amino acids may be used in these segments. Finally,while it is possible to base the designed composition of the N1 and N2segments of the invention on the composition of naturally occurring N1and N2 segments, this is not a requirement. The N1 and N2 segments maycomprise amino acids selected from any group of amino acids, or designedaccording to other criteria considered for the design of a library ofthe invention. A person of ordinary skill in the art would readilyrecognize that the criteria used to design any portion of a library ofthe invention may vary depending on the application of the particularlibrary. It is an object of the invention that it may be possible toproduce a functional library through the use of N1 and N2 segmentsselected from any group of amino acids, no N1 or N2 segments, or the useof N1 and N2 segments with compositions other than those describedherein.

One important difference between the libraries of the current inventionand other libraries known in the art is the consideration of thecomposition of naturally occurring duplet and triplet amino acidsequences during the design of the library. Table 23 shows the toptwenty-five naturally occurring duplets in the N1 and N2 regions. Manyof these can be represented by the general formula(G/P)(G/R/S/P/L/A/V/T) or (R/S/L/A/V/T)(G/P). In certain embodiments ofthe invention, the synthetic N1 and N2 regions may comprise all of theseduplets. In other embodiments, the library may comprise the top 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, or 25 most common naturally occurring N1 and/or N2 duplets. In otherembodiments of the invention, the libraries may include duplets that areless frequently occurring (i.e., outside of the top 25). The compositionof these additional duplets or triplets could readily be determined,given the methods taught herein.

Finally, the data from the naturally occurring triplet N1 and N2 regionsdemonstrates that the naturally occurring N1 and N2 triplet sequencescan often be represented by the formulas (G)(G)(G/R/S/P/L/A/V/T),(G)(R/S/P/L/A/V/T)(G), or (R/S/P/L/A/V/T)(G)(G). In certain embodimentsof the invention, the library may comprise the top 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25most commonly occurring N1 and/or N2 triplets. In other embodiments ofthe invention, the libraries may include triplets that are lessfrequently occurring (i.e., outside of the top 25). The composition ofthese additional duplets or triplets could readily be determined, giventhe methods taught herein.

In certain embodiments of the invention, there are about 59 total N1segments and about 59 total N2 segments used to create a library ofCDRH3s. In other embodiments of the invention, the number of N1segments, N2 segments, or both is increased to about 141 (see, forexample, Example 5). In other embodiments of the invention, one mayselect a total of about 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170,180, 190, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400, 420,440, 460, 480, 500, 1000, 10⁴, or more N1 and/or N2 segments forinclusion in a library of the invention.

One of ordinary skill in the art will readily recognize that, given theteachings of the instant specification, it is well within the realm ofnormal experimentation to extend the analysis detailed herein, forexample, to generate additional rankings of naturally occurring dupletand triplet (or higher order) N regions that extend beyond thosepresented herein (e.g., using sequence alignment, the SoDA algorithm,and any database of human sequences (Volpe et al., Bioinformatics, 2006,22: 438-44, incorporated by reference in its entirety). An ordinarilyskilled artisan would also recognize that, based on the informationtaught herein, it is now possible to produce libraries that are morediverse or less diverse (i.e., more focused) by varying the number ofdistinct amino acid sequences used in the N1 pool and/or N2 pool.

As described above, many alternative embodiments are envisioned, inwhich the compositions and lengths of the N1 and N2 segments vary fromthose presented in the Examples herein. In some embodiments,sub-stoichiometric synthesis of trinucleotides may be used for thesynthesis of N1 and N2 segments. Sub-stoichiometric synthesis withtrinucleotides is described in Knappik et al. (U.S. Pat. No. 6,300,064,incorporated by reference in its entirety). The use ofsub-stoichiometric synthesis would enable synthesis with considerationof the length variation in the N1 and N2 sequences.

In addition to the embodiments described above, a model of the activityof TdT may also be used to determine the composition of the N1 and N2sequences in a library of the invention. For example, it has beenproposed that the probability of incorporating a particular nucleotidebase (A, C, G, T) on a polynucleotide, by the activity of TdT, isdependent on the type of base and the base that occurs on the stranddirectly preceding the base to be added. Jackson et al., (J. Immunol.Methods, 2007, 324: 26, incorporated by reference in its entirety) haveconstructed a Markov model describing this process. In certainembodiments of the invention, this model may be used to determine thecomposition of the N1 and/or N2 segments used in libraries of theinvention. Alternatively, the parameters presented in Jackson et al.could be further refined to produce sequences that more closely mimichuman sequences.

2.2.4. Design of a CDRH3 Library Using the N1, DH, N2, and H3-JHSegments

The CDRH3 libraries of the invention comprise an initial amino acid (incertain exemplary embodiments, G, D, E) or lack thereof (designatedherein as position 95), followed by the N1, DH, N2, and H3-JH segments.Thus, in certain embodiments of the invention, the overall design of theCDRH3 libraries can be represented by the following formula:

[G/D/E/-]-[N1]-[DH]-[N2]-[H3-JH].

While the compositions of each portion of a CDRH3 of a library of theinvention are more fully described above, the composition of the tailpresented above (G/D/E/-) is non-limiting, and that any amino acid (orno amino acid) can be used in this position. Thus, certain embodimentsof the invention may be represented by the following formula:

[X]-[N1]-[DH]-[N2]-[H3-JH],

wherein [X] is any amino acid residue or no residue.

In certain embodiments of the invention, a synthetic CDRH3 repertoire iscombined with selected VH chassis sequences and heavy chain constantregions, via homologous recombination. Therefore, in certain embodimentsof the invention, it may be necessary to include DNA sequences flankingthe 5′ and 3′ ends of the synthetic CDRH3 libraries, to facilitatehomologous recombination between the synthetic CDRH3 libraries andvectors containing the selected chassis and constant regions. In certainembodiments, the vectors also contain a sequence encoding at least aportion of the non-nibbled region of the IGHJ gene (i.e., FRM4-JH).Thus, a polynucleotide encoding an N-terminal sequence (e.g., CA(K/R/T))may be added to the synthetic CDRH3 sequences, wherein the N-terminalpolynucleotide is homologous with FRM3 of the chassis, while apolynucleotide encoding a C-terminal sequence (e.g., WG(Q/R)G; SEQ IDNO: 23) may be added to the synthetic CDRH3, wherein the C-terminalpolynucleotide is homologous with FRM4-JH. Although the sequenceWG(Q/R)G (SEQ ID NO: 23) is presented in this exemplary embodiment,additional amino acids, C-terminal to this sequence in FRM4-JH may alsobe included in the polynucleotide encoding the C-terminal sequence. Thepurpose of the polynucleotides encoding the N-terminal and C-terminalsequences, in this case, is to facilitate homologous recombination, andone of ordinary skill in the art would recognize that these sequencesmay be longer or shorter than depicted below. Accordingly, in certainembodiments of the invention, the overall design of the CDRH3repertoire, including the sequences required to facilitate homologousrecombination with the selected chassis, can be represented by thefollowing formula (regions homologous with vector underlined):

CA[R/K/T]-[X]-[N1]-[DH]-[N2]-[H3-JH]-[WG(Q/R)G].

In other embodiments of the invention, the CDRH3 repertoire can berepresented by the following formula, which excludes the T residuepresented in the schematic above:

CA[R/K]-[X]-[N1]-[DH]-[N2]-[H3-JH]-[WG(Q/R)G].

References describing collections of V, D, and J genes include Scavineret al., Exp. Clin, Immunogenet., 1999, 16: 243 and Ruiz et al., Exp.Clin Immunogenet, 1999, 16: 173, each incorporated by reference in itsentirety.

2.2.5. CDRH3 Length Distributions

As described throughout this application, in addition to accounting forthe composition of naturally occurring CDRH3 segments, the instantinvention also takes into account the length distribution of naturallyoccurring CDRH3 segments. Surveys by Zemlin et al. (JMB, 2003, 334: 733,incorporated by reference in its entirety) and Lee et al.(Immunogenetics, 2006, 57: 917, incorporated by reference in itsentirety) provide analyses of the naturally occurring CDRH3 lengths.These data show that about 95% of naturally occurring CDRH3 sequenceshave a length from about 7 to about 23 amino acids. In certainembodiments, the instant invention provides rationally designed antibodylibraries with CDRH3 segments which directly mimic the size distributionof naturally occurring CDRH3 sequences. In certain embodiments of theinvention, the length of the CDRH3s may be about 2 to about 30, about 3to about 35, about 7 to about 23, about 3 to about 28, about 5 to about28, about 5 to about 26, about 5 to about 24, about 7 to about 24, about7 to about 22, about 8 to about 19, about 9 to about 22, about 9 toabout 20, about 10 to about 18, about 11 to about 20, about 11 to about18, about 13 to about 18, or about 13 to about 16 residues in length.

In certain embodiments of the invention, the length distribution of aCDRH3 library of the invention may be defined based on the percentage ofsequences within a certain length range. For example, in certainembodiments of the invention, CDRH3s with a length of about 10 to about18 amino acid residues comprise about 84% to about 94% of the sequencesof a the library. In some embodiments, sequences within this lengthrange comprise about 89% of the sequences of a library.

In other embodiments of the invention, CDRH3s with a length of about 11to about 17 amino acid residues comprise about 74% to about 84% of thesequences of a library. In some embodiments, sequences within thislength range comprise about 79% of the sequences of a library.

In still other embodiments of the invention, CDRH3s with a length ofabout 12 to about 16 residues comprise about 57% to about 67% of thesequences of a library. In some embodiments, sequences within thislength range comprise about 62% of the sequences of a library.

In certain embodiments of the invention, CDRH3s with a length of about13 to about 15 residues comprise about 35% to about 45% of the sequencesof a library. In some embodiments, sequences within this length rangecomprise about 40% of the sequences of a library.

2.3. Design of the Antibody Library CDRL3 Components

The CDRL3 libraries of the invention can be generated by one of severalapproaches. The actual version of the CDRL3 library made and used in aparticular embodiment of the invention will depend on objectives for theuse of the library. More than one CDRL3 library may be used in aparticular embodiment; for example, a library containing CDRH3diversity, with kappa and lambda light chains is within the scope of theinvention.

In certain embodiments of the invention, a CDRL3 library is a VKCDR3(kappa) library and/or a VλCDR3 (lambda) library. The CDRL3 librariesdescribed herein differ significantly from CDRL3 libraries in the art.First, they consider length variation that is consistent with what isobserved in actual human sequences. Second, they take into considerationthe fact that a significant portion of the CDRL3 is encoded by the IGLVgene. Third, the patterns of amino acid variation within the IGLVgene-encoded CDRL3 portions are not stochastic and are selected based ondepending on the identity of the IGLV gene. Taken together, the secondand third distinctions mean that CDRL3 libraries that faithfully mimicobserved patterns in human sequences cannot use a generic design that isindependent of the chassis sequences in FRM1 to FRM3. Fourth, thecontribution of JL to CDRL3 is also considered explicitly, andenumeration of each amino acid residue at the relevant positions isbased on the compositions and natural variations of the JL genesthemselves.

As indicated above, and throughout the application, a unique aspect ofthe design of the libraries of the invention is the germline or“chassis-based” aspect, which is meant to preserve more of the integrityand variability of actual human sequences. This is in contrast to othercodon-based synthesis or degenerate oligonucleotide synthesis approachesthat have been described in the literature and that aim to produce“one-size-fits-all” (e.g., consensus) libraries (e.g. Knappik, et al., JMol Biol, 2000, 296: 57; Akamatsu et al., J Immunol, 1993, 151: 4651,each incorporated by reference in its entirety).

In certain embodiments of the invention, patterns of occurrence ofparticular amino acids at defined positions within VL sequences aredetermined by analyzing data available in public or other databases, forexample, the NCBI database (see, for example, GI numbers in Appendices Aand B filed herewith). In certain embodiments of the invention, thesesequences are compared on the basis of identity and assigned to familieson the basis of the germline genes from which they are derived. Theamino acid composition at each position of the sequence, in eachgermline family, may then be determined. This process is illustrated inthe Examples provided herein.

2.3.1. Minimalist VKCDR3 Libraries

In certain embodiments of the invention, the light chain CDR3 library isa VKCDR3 library. Certain embodiments of the invention may use only themost common VKCDR3 length, nine residues; this length occurs in adominant proportion (greater than about 70%) of human VKCDR3 sequences.In human VKCDR3 sequences of length nine, positions 89-95 are encoded bythe IGKV gene and positions 96-97 are encoded by the IGKJ gene. Analysisof human kappa light chain sequences indicates that there are not strongbiases in the usage of the IGKJ genes. Therefore, in certain embodimentsof the invention, each of the five the IGKJ genes can be represented inequal proportions to create a combinatorial library of (M VK chassis)×(5JK genes), or a library of size M×5. However, in other embodiments ofthe invention, it may be desirable to bias IGKJ gene representation, forexample to restrict the size of the library or to weight the librarytoward IGKJ genes known to have particular properties.

As described in Example 6.1, examination of the first amino acid encodedby the IGKJ gene (position 96) indicated that the seven most commonresidues found at this position are L, Y, R, W, F, P, and I. Theseresidues cumulatively account for about 85% of the residues found inposition 96 in naturally occurring kappa light chain sequences. Incertain embodiments of the invention, the amino acid residue at position96 may be one of these seven residues. In other embodiments of theinvention, the amino acid at this position may be chosen from amongstany of the other 13 amino acid residues. In still other embodiments ofthe invention, the amino acid residue at position 96 may be chosen fromamongst the top 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, or 20 amino acids that occur at position 96, or evenresidues that never occur at position 96. Similarly, the occurrence ofthe amino acids selected to occupy position 96 may be equivalent orweighted. In certain embodiments of the invention, it may be desirableto include each of the amino acids selected for inclusion in position 96at equivalent amounts. In other embodiments of the invention, it may bedesirable to bias the composition of position 96 to include particularresidues more or less frequently than others. For example, as presentedin Example 6.1, arginine occurs at position 96 most frequently when theIGKJ1 (SEQ ID NO: 552) germline sequence is used. Therefore, in certainembodiments of the invention, it may be desirable to bias amino acidusage at position 96 according to the origin of the IGKJ germlinesequence(s) and/or the IGKV germline sequence(s) selected forrepresentation in a library.

Therefore, in certain embodiments of the invention, a minimalist VKCDR3library may be represented by one or more of the following amino acidsequences:

[VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[JK*]

[VK_Chassis]-[L3-VK]-[X]-[JK*]

In these schematic exemplary sequences, VK_Chassis represents any VKchassis selected for inclusion in a library of the invention (e.g., seeTable 11). Specifically, VK_Chassis comprises about Kabat residues 1 to88 of a selected IGKV sequence. L3-VK represents the portion of theVKCDR3 encoded by the chosen IGKV gene (in this embodiment, Kabatresidues 89-95). F, L, I, R, W, Y, and P are the seven most commonlyoccurring amino acids at position 96 of VKCDR3s with length nine, X isany amino acid, and JK* is an IGKJ amino acid sequence without theN-terminal residue (i.e., the N-terminal residue is substituted with F,L, I, R, W, Y, P, or X). Thus, in one possible embodiment of theminimalist VKCDR3 library, 70 members could be produced by utilizing 10VK chassis, each paired with its respective L3-VK, 7 amino acids atposition 96 (i.e., X), and one JK* sequence. Another embodiment of thelibrary may have 350 members, produced by combining 10 VK chassis, eachpaired with its respective L3-VK, with 7 amino acids at position 96, andall 5 JK* genes. Still another embodiment of the library may have 1,125members, produced by combining 15 VK chassis, each paired with itsrespective H3-JK, with 15 amino acids at position 96 and all 5 JK*genes, and so on. A person of ordinary skill in the art will readilyrecognize that many other combinations are possible. Moreover, while itis believed that maintaining the pairing between the VK chassis and theL3-VK results in libraries that are more similar to human kappa lightchain sequences in composition, the L3-VK regions may also becombinatorially varied with different VK chassis regions, to createadditional diversity.

2.3.2. VKCDR3 Libraries of About 10⁵ Complexity

While the dominant length of VKCDR3 sequences in humans is about nineamino acids, other lengths appear at measurable frequencies thatcumulatively approach almost about 30% of VKCDR3 sequences. Inparticular, VKCDR3 of lengths 8 and 10 represent about 8.5% and about16%, respectively, of VKCDR3 lengths in representative samples (Example6.2; FIG. 3). Thus, more complex VKCDR3 libraries may include CDRlengths of 8, 10, and 11 amino acids. Such libraries could account for agreater percentage of the length distribution observed in collections ofhuman VKCDR3 sequences, or even introduce VKCDR3 lengths that do notoccur frequently in human VKCDR3 sequences (e.g., less than eightresidues or greater than 11 residues).

The inclusion of a diversity of kappa light chain length variations in alibrary of the invention also enables one to include sequencevariability that occurs outside of the amino acid at the VK-JK junction(i.e., position 96, described above). In certain embodiments of theinvention, the patterns of sequence variation within the VK, and/or JKsegments can be determined by aligning collections of sequences derivedfrom particular germline sequences. In certain embodiments of theinvention, the frequency of occurrence of amino acid residues withinVKCDR3 can be determined by sequence alignments (e.g., see Example 6.2and Table 30). In some embodiments of the invention, this frequency ofoccurrence may be used to introduce variability into the VK_Chassis,L3-VK and/or JK segments that are used to synthesize the VKCDR3libraries. In certain embodiments of the invention, the top 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acidsthat occur at any particular position in a naturally occurringrepertoire may be included at that position in a VKCDR3 library of theinvention. In certain embodiments of the invention, the percentoccurrence of any amino acid at any particular position within theVKCDR3 or a VK light chain may be about 0%, 1%, 2%, 3%, 4%, 5%, 6%, 7%,8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, or 100%. In certain embodiments of theinvention, the percent occurrence of any amino acid at any positionwithin a VKCDR3 or kappa light chain library of the invention may bewithin at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% 10%, 15%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 120%, 140%, 160%, 180%, or 200%of the percent occurrence of any amino acid at any position within anaturally occurring VKCDR3 or kappa light chain domain.

In some embodiments of the invention, a VKCDR3 library may besynthesized using degenerate oligonucleotides (see Table 31 for IUPACbase symbol definitions). In some embodiments of the invention, thelimits of oligonucleotide synthesis and the genetic code may require theinclusion of more or fewer amino acids at a particular position in theVKCDR3 sequences. An illustrative embodiment of this approach isprovided in Example 6.2.

2.3.3. More Complex VKCDR3 Libraries

The limitations inherent in using the genetic code and degenerateoligonucleotide synthesis may, in some cases, require the inclusion ofmore or fewer amino acids at a particular position within VKCDR3 (e.g.,Example 6.2, Table 32), in comparison to those amino acids found at thatposition in nature. This limitation can be overcome through the use of acodon-based synthesis approach (Virnekas et al. Nucleic Acids Res.,1994, 22: 5600, incorporated by reference in its entirety), whichenables precise synthesis of oligonucleotides encoding particular aminoacids and a finer degree of control over the proportion of anyparticular amino acid incorporated at any position. Example 6.3describes this approach in greater detail.

In some embodiments of the invention, a codon-based synthesis approachmay be used to vary the percent occurrence of any amino acid at anyparticular position within the VKCDR3 or kappa light chain. In certainembodiments, the percent occurrence of any amino acid at any position ina VKCDR3 or kappa light chain sequence of the library may be about 0%,1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%. In someembodiments of the invention, the percent occurrence of any amino acidat any position may be about 1%, 2%, 3%, or 4%. In certain embodimentsof the invention, the percent occurrence of any amino acid at anyposition within a VKCDR3 or kappa light chain library of the inventionmay be within at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%,15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 120%, 140%, 160%,180%, or 200% of the percent occurrence of any amino acid at anyposition within a naturally occurring VKCDR3 or kappa light chaindomain.

In certain embodiments of the invention, the VKCDR3 (and any othersequence used in the library, regardless of whether or not it is part ofVKCDR3) may be altered to remove undesirable amino acid motifs. Forexample, peptide sequences with the pattern N-X-(S or T)-Z, where X andZ are different from P, will undergo post-translational modification(N-linked glycosylation) in a number of expression systems, includingyeast and mammalian cells. In certain embodiments of the invention, theintroduction of N residues at certain positions may be avoided, so as toavoid the introduction of N-linked glycosylation sites. In someembodiments of the invention, these modifications may not be necessary,depending on the organism used to express the library and the cultureconditions. However, even in the event that the organism used to expresslibraries with potential N-linked glycosylation sites is incapable ofN-linked glycosylation (e.g., bacteria), it may still be desirable toavoid N-X-(S/T) sequences, as the antibodies isolated from suchlibraries may be expressed in different systems (e.g., yeast, mammaliancells) later (e.g., toward clinical development), and the presence ofcarbohydrate moieties in the variable domains, and the CDRs inparticular, may lead to unwanted modifications of activity.

In certain embodiments of the invention, it may be preferable to createthe individual sub-libraries of different lengths (e.g., one or more oflengths 5, 6, 7, 8, 9, 10, 11, or more) separately, and then mix thesub-libraries in proportions that reflect the length distribution ofVKCDR3 in human sequences; for example, in ratios approximating the1:9:2 distribution that occurs in natural VKCDR3 sequences of lengths 8,9, and 10 (see FIG. 3). In other embodiments, it may be desirable to mixthese sub-libraries at ratios that are different from the distributionof lengths in natural VKCDR3 sequences, for example, to produce morefocused libraries or libraries with particular properties.

2.3.4. VλCDR3 Libraries

The principles used to design the minimalist VλCDR3 libraries of theinvention are similar to those enumerated above, for the VKCDR3libraries, and are explained in more detail in the Examples. Onedifference between the VλCDR3 libraries of the invention and the VKCDR3libraries of the invention is that, unlike the IGKV genes, thecontribution of the IGVλ genes to CDRL3 (i.e., L3-Vλ) is not constrainedto a fixed number of amino acid residues. Therefore, while thecombination of the VK (including L3-VK) and JK segments, with inclusionof position 96, yields CDRL3 with a length of only 9 residues, lengthvariation may be obtained within a VλCDR3 library even when only the Vλ(including L3-Vλ) and Jλ segments are considered.

As for the VKCDR3 sequences, additional variability may be introducedinto the VλCDR3 sequences via the same methods outlined above, namelydetermining the frequency of occurrence of particular residues withinVλCDR3 sequences and synthesizing the oligonucleotides encoding thedesired compositions via degenerate oligonucleotide synthesis ortrinucleotides-based synthesis.

2.4. Synthetic Antibody Libraries

In certain embodiments of the invention, both the heavy and light chainchassis sequences and the heavy and light chain CDR3 sequences aresynthetic. The polynucleotide sequences of the instant invention can besynthesized by various methods. For example, sequences can besynthesized by split pool DNA synthesis as described in Feldhaus et al.,Nucleic Acids Research, 2000, 28: 534; Omstein et al., Biopolymers,1978, 17: 2341; and Brenner and Lerner, PNAS, 1992, 87: 6378 (each ofwhich is incorporated by reference in its entirety).

In some embodiments of the invention, cassettes representing thepossible V, D, and J diversity found in the human repertoire, as well asjunctional diversity, are synthesized de novo either as double-strandedDNA oligonucleotides, single-stranded DNA oligonucleotidesrepresentative of the coding strand, or single-stranded DNAoligonucleotides representative of the non-coding strand. Thesesequences can then be introduced into a host cell along with an acceptorvector containing a chassis sequence and, in some cases a portion ofFRM4 and a constant region. No primer-based PCR amplification frommammalian cDNA or mRNA or template-directed cloning steps from mammaliancDNA or mRNA need be employed.

2.5. Construction of Libraries by Yeast Homologous Recombination

In certain embodiments, the present invention exploits the inherentability of yeast cells to facilitate homologous recombination at highefficiency. The mechanism of homologous recombination in yeast and itsapplications are briefly described below.

As an illustrative embodiment, homologous recombination can be carriedout in, for example, Saccharomyces cerevisiae, which has geneticmachinery designed to carry out homologous recombination with highefficiency. Exemplary S. cerevisiae strains include EM93, CEN.PK2,RM11-1a, YJM789, and BJ5465. This mechanism is believed to have evolvedfor the purpose of chromosomal repair, and is also called “gap repair”or “gap filling”. By exploiting this mechanism, mutations can beintroduced into specific loci of the yeast genome. For example, a vectorcarrying a mutant gene can contain two sequence segments that arehomologous to the 5′ and 3′ open reading frame (ORF) sequences of a genethat is intended to be interrupted or mutated. The vector may alsoencode a positive selection marker, such as a nutritional enzyme allele(e.g., URA3) and/or an antibiotic resistant marker (e.g.,Geneticin/G418), flanked by the two homologous DNA segments. Otherselection markers and antibiotic resistance markers are known to one ofordinary skill in the art. In some embodiments of the invention, thisvector (e.g., a plasmid) is linearized and transformed into the yeastcells. Through homologous recombination between the plasmid and theyeast genome, at the two homologous recombination sites, a reciprocalexchange of the DNA content occurs between the wild type gene in theyeast genome and the mutant gene (including the selection markergene(s)) that is flanked by the two homologous sequence segments. Byselecting for the one or more selection markers, the surviving yeastcells will be those cells in which the wild-type gene has been replacedby the mutant gene (Pearson et al., Yeast, 1998, 14: 391, incorporatedby reference in its entirety). This mechanism has been used to makesystematic mutations in all 6,000 yeast genes, or open reading frames(ORFs), for functional genomics studies. Because the exchange isreciprocal, a similar approach has also been used successfully to cloneyeast genomic DNA fragments into a plasmid vector (Iwasaki et al., Gene,1991, 109: 81, incorporated by reference in its entirety).

By utilizing the endogenous homologous recombination machinery presentin yeast, gene fragments or synthetic oligonucleotides can also becloned into a plasmid vector without a ligation step. In thisapplication of homologous recombination, a target gene fragment (i.e.,the fragment to be inserted into a plasmid vector, e.g., a CDR3) isobtained (e.g., by oligonucleotides synthesis, PCR amplification,restriction digestion out of another vector, etc.). DNA sequences thatare homologous to selected regions of the plasmid vector are added tothe 5′ and 3′ ends of the target gene fragment. These homologous regionsmay be fully synthetic, or added via PCR amplification of a target genefragment with primers that incorporate the homologous sequences. Theplasmid vector may include a positive selection marker, such as anutritional enzyme allele (e.g., URA3), or an antibiotic resistancemarker (e.g., Geneticin/G418). The plasmid vector is then linearized bya unique restriction cut located in-between the regions of sequencehomology shared with the target gene fragment, thereby creating anartificial gap at the cleavage site. The linearized plasmid vector andthe target gene fragment flanked by sequences homologous to the plasmidvector are co-transformed into a yeast host strain. The yeast is thenable to recognize the two stretches of sequence homology between thevector and target gene fragment and facilitate a reciprocal exchange ofDNA content through homologous recombination at the gap. As aconsequence, the target gene fragment is inserted into the vectorwithout ligation.

The method described above has also been demonstrated to work when thetarget gene fragments are in the form of single stranded DNA, forexample, as a circular M13 phage derived form, or as single strandedoligonucleotides (Simon and Moore, Mol. Cell Biol., 1987, 7: 2329;Ivanov et al., Genetics, 1996, 142: 693; and DeMarini et al., 2001, 30:520., each incorporated by reference in its entirety). Thus, the form ofthe target that can be recombined into the gapped vector can be doublestranded or single stranded, and derived from chemical synthesis, PCR,restriction digestion, or other methods.

Several factors may influence the efficiency of homologous recombinationin yeast. For example, the efficiency of the gap repair is correlatedwith the length of the homologous sequences flanking both the linearizedvector and the target gene. In certain embodiments, about 20 or morebase pairs may be used for the length of the homologous sequence, andabout 80 base pairs may give a near-optimized result (Hua et al.,Plasmid, 1997, 38: 91; Raymond et al., Genome Res., 2002, 12: 190, eachincorporated by reference in its entirety). In certain embodiments ofthe invention, at least about 5, 10, 15, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180,187, 190, or 200 homologous base pairs may be used to facilitaterecombination. In other embodiments, between about 20 and about 40 basepairs are utilized. In addition, the reciprocal exchange between thevector and gene fragment is strictly sequence-dependent, i.e. it doesnot cause a frame shift. Therefore, gap-repair cloning assures theinsertion of gene fragments with both high efficiency and precision. Thehigh efficiency makes it possible to clone two, three, or more targetedgene fragments simultaneously into the same vector in one transformationattempt (Raymond et al., Biotechniques, 1999, 26: 134, incorporated byreference in its entirety). Moreover, the nature of precision sequenceconservation through homologous recombination makes it possible to cloneselected genes or gene fragments into expression or fusion vectors fordirect functional examination (El-Deiry et al., Nature Genetics, 1992,1: 4549; Ishioka et al., PNAS, 1997, 94: 2449, each incorporated byreference in its entirety).

Libraries of gene fragments have also been constructed in yeast usinghomologous recombination. For example, a human brain cDNA library wasconstructed as a two-hybrid fusion library in vector pJG4-5 (Guidottiand Zervos, Yeast, 1999, 15: 715, incorporated by reference in itsentirety). It has also been reported that a total of 6,000 pairs of PCRprimers were used for amplification of 6,000 known yeast ORFs for astudy of yeast genomic protein interactions (Hudson et al., Genome Res.,1997, 7: 1169, incorporated by reference in its entirety). In 2000, Uetzet al. conducted a comprehensive analysis-of protein-proteininteractions in Saccharomyces cerevisiae (Uetz et al., Nature, 2000,403: 623, incorporated by reference in its entirety). Theprotein-protein interaction map of the budding yeast was studied byusing a comprehensive system to examine two-hybrid interactions in allpossible combinations between the yeast proteins (Ito et al., PNAS,2000, 97: 1143, incorporated by reference in its entirety), and thegenomic protein linkage map of Vaccinia virus was studied using thissystem (McCraith et al., PNAS, 2000, 97: 4879, incorporated by referencein its entirety).

In certain embodiments of the invention, a synthetic CDR3 (heavy orlight chain) may be joined by homologous recombination with a vectorencoding a heavy or light chain chassis, a portion of FRM4, and aconstant region, to form a full-length heavy or light chain. In certainembodiments of the invention, the homologous recombination is performeddirectly in yeast cells. In some embodiments, the method comprises:

-   -   (a) transforming into yeast cells:        -   (i) a linearized vector encoding a heavy or light chain            chassis, a portion of FRM4, and a constant region, wherein            the site of linearization is between the end of FRM3 of the            chassis and the beginning of the constant region; and        -   (ii) a library of CDR3 insert nucleotide sequences that are            linear and double stranded, wherein each of the CDR3 insert            sequences comprises a nucleotide sequence encoding CDR3 and            5′- and 3′-flanking sequences that are sufficiently            homologous to the termini of the vector of (i) at the site            of linearization to enable homologous recombination to occur            between the vector and the library of CDR3 insert sequences;            and    -   (b) allowing homologous recombination to occur between the        vector and the CDR3 insert sequences in the transformed yeast        cells, such that the CDR3 insert sequences are incorporated into        the vector, to produce a vector encoding full-length heavy chain        or light chain.

As specified above, the CDR3 inserts may have a 5′ flanking sequence anda 3′ flanking sequence that are homologous to the termini of thelinearized vector. When the CDR3 inserts and the linearized vectors areintroduced into a host cell, for example, a yeast cell, the “gap” (thelinearization site) created by linearization of the vector is filled bythe CDR3 fragment insert through recombination of the homologoussequences at the 5′ and 3′ termini of these two linear double-strandedDNAs (i.e., the vector and the insert). Through this event of homologousrecombination, libraries of circular vectors encoding full-length heavyor light chains comprising variable CDR3 inserts is generated.Particular instances of these methods are presented in the Examples.

Subsequent analysis may be carried out to determine the efficiency ofhomologous recombination that results in correct insertion of the CDR3sequences into the vectors. For example, PCR amplification of the CDR3inserts directly from selected yeast clones may reveal how many clonesare recombinant. In certain embodiments, libraries with minimum of about90% recombinant clones are utilized. In certain other embodimentslibraries with a minimum of about 1%, 5% 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% recombinant clonesare utilized. The same PCR amplification of selected clones may alsoreveal the insert size.

To verify the sequence diversity of the inserts in the selected clones,a PCR amplification product with the correct size of insert may be“fingerprinted” with restriction enzymes known to cut or not cut withinthe amplified region. From a gel electrophoresis pattern, it may bedetermined whether the clones analyzed are of the same identity or ofthe distinct or diversified identity. The PCR products may also besequenced directly to reveal the identity of inserts and the fidelity ofthe cloning procedure, and to prove the independence and diversity ofthe clones. FIG. 1 depicts a schematic of recombination between afragment (e.g., CDR3) and a vector (e.g., comprising a chassis, portionof FRM4, and constant region) for the construction of a library.

2.6. Expression and Screening Systems

Libraries of polynucleotides generated by any of the techniquesdescribed herein, or other suitable techniques, can be expressed andscreened to identify antibodies having desired structure and/oractivity. Expression of the antibodies can be carried out, for example,using cell-free extracts (and e.g., ribosome display), phage display,prokaryotic cells (e.g., bacterial display), or eukaryotic cells (e.g.,yeast display). In certain embodiments of the invention, the antibodylibraries are expressed in yeast.

In other embodiments, the polynucleotides are engineered to serve astemplates that can be expressed in a cell-free extract. Vectors andextracts as described, for example in U.S. Pat. Nos. 5,324,637;5,492,817; 5,665,563, (each incorporated by reference in its entirety)can be used and many are commercially available. Ribosome display andother cell-free techniques for linking a polynucleotide (i.e., agenotype) to a polypeptide (i.e., a phenotype) can be used, e.g.,Profusion™ (see, e.g., U.S. Pat. Nos. 6,348,315; 6,261,804; 6,258,558;and 6,214,553, each incorporated by reference in its entirety).

Alternatively, the polynucleotides of the invention can be expressed inan E. coli expression system, such as that described by Pluckthun andSkerra. (Meth. Enzymol., 1989, 178: 476; Biotechnology, 1991, 9: 273,each incorporated by reference in its entirety). The mutant proteins canbe expressed for secretion in the medium and/or in the cytoplasm of thebacteria, as described by Better and Horwitz, Meth. Enzymol., 1989, 178:476, incorporated by reference in its entirety. In some embodiments, thesingle domains encoding VH and VL are each attached to the 3′ end of asequence encoding a signal sequence, such as the ompA, phoA or pelBsignal sequence (Lei et al., J. Bacteriol., 1987, 169: 4379,incorporated by reference in its entirety). These gene fusions areassembled in a dicistronic construct, so that they can be expressed froma single vector, and secreted into the periplasmic space of E. coliwhere they will refold and can be recovered in active form. (Skerra etal., Biotechnology, 1991, 9: 273, incorporated by reference in itsentirety). For example, antibody heavy chain genes can be concurrentlyexpressed with antibody light chain genes to produce antibodies orantibody fragments.

In other embodiments of the invention, the antibody sequences areexpressed on the membrane surface of a prokaryote, e.g., E. coli, usinga secretion signal and lipidation moiety as described, e.g., inUS20040072740; US20030100023; and US20030036092 (each incorporated byreference in its entirety).

Higher eukaryotic cells, such as mammalian cells, for example myelomacells (e.g., NS/0 cells), hybridoma cells, Chinese hamster ovary (CHO),and human embryonic kidney (HEK) cells, can also be used for expressionof the antibodies of the invention. Typically, antibodies expressed inmammalian cells are designed to be secreted into the culture medium, orexpressed on the surface of the cell. The antibody or antibody fragmentscan be produced, for example, as intact antibody molecules or asindividual VH and VL fragments, Fab fragments, single domains, or assingle chains (scFv) (Huston et al., PNAS, 1988, 85: 5879, incorporatedby reference in its entirety).

Alternatively, antibodies can be expressed and screened by anchoredperiplasmic expression (APEx 2-hybrid surface display), as described,for example, in Jeong et al., PNAS, 2007, 104: 8247 (incorporated byreference in its entirety) or by other anchoring methods as described,for example, in Mazor et al., Nature Biotechnology, 2007, 25: 563(incorporated by reference in its entirety).

In other embodiments of the invention, antibodies can be selected usingmammalian cell display (Ho et al., PNAS, 2006, 103: 9637, incorporatedby reference in its entirety).

The screening of the antibodies derived from the libraries of theinvention can be carried out by any appropriate means. For example,binding activity can be evaluated by standard immunoassay and/oraffinity chromatography. Screening of the antibodies of the inventionfor catalytic function, e.g., proteolytic function can be accomplishedusing a standard assays, e.g., the hemoglobin plaque assay as describedin U.S. Pat. No. 5,798,208 (incorporated by reference in its entirety).Determining the ability of candidate antibodies to bind therapeutictargets can be assayed in vitro using, e.g., a BIACORE™ instrument,which measures binding rates of an antibody to a given target or antigenbased on surface plasmon resonance. In vivo assays can be conductedusing any of a number of animal models and then subsequently tested, asappropriate, in humans. Cell-based biological assays are alsocontemplated.

One aspect of the instant invention is the speed at which the antibodiesof the library can be expressed and screened. In certain embodiments ofthe invention, the antibody library can be expressed in yeast, whichhave a doubling time of less than about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 hours. In someembodiments, the doubling times are about 1 to about 3 hours, about 2 toabout 4, about 3 to about 8 hours, about 3 to about 24, about 5 to about24, about 4 to about 6 about 5 to about 22, about 6 to about 8, about 7to about 22, about 8 to about 10 hours, about 7 to about 20, about 9 toabout 20, about 9 to about 18, about 11 to about 18, about 11 to about16, about 13 to about 16, about 16 to about 20, or about 20 to about 30hours. In certain embodiments of the invention, the antibody library isexpressed in yeast with a doubling time of about 16 to about 20 hours,about 8 to about 16 hours, or about 4 to about 8 hours. Thus, theantibody library of the instant invention can be expressed and screenedin a matter of hours, as compared to previously known techniques whichtake several days to express and screen antibody libraries. A limitingstep in the throughput of such screening processes in mammalian cells issimply the time required to iteratively regrow populations of isolatedcells, which, in some cases, have doubling times greater than thedoubling times of the yeast used in the current invention.

In certain embodiments of the invention, the composition of a librarymay be defined after one or more enrichment steps (for example byscreening for antigen binding, or other properties). For example, alibrary with a composition comprising about x % sequences or librariesof the invention may be enriched to contain about 2x %, 3x %, 4x %, 5x%, 6x %, 7x %, 8x %, 9x %, 10x %, 20x %, 25x %, 40x %, 50x %, 60x % 75x%, 80x %, 90x %, 95x %, or 99x % sequences or libraries of theinvention, after one or more screening steps. In other embodiments ofthe invention, the sequences or libraries of the invention may beenriched about 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold,9-fold, 10-fold, 100-fold, 1,000-fold, or more, relative to theiroccurrence prior to the one or more enrichment steps. In certainembodiments of the invention, a library may contain at least a certainnumber of a particular type of sequence(s), such as CDRH3s, CDRL3s,heavy chains, light chains, or whole antibodies (e.g., at least about10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵,10¹⁶, 10¹⁷, 10¹⁸, 10¹⁹, or 10²⁰). In certain embodiments, thesesequences may be enriched during one or more enrichment steps, toprovide libraries comprising at least about 10², 10³, 10⁴, 10⁵, 10⁶,10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁷, 10¹⁸, or10¹⁹ of the respective sequence(s).

2.7. Mutagenesis Approaches for Affinity Maturation

As described above, antibody leads can be identified through a selectionprocess that involves screening the antibodies of a library of theinvention for binding to one or more antigens, or for a biologicalactivity. The coding sequences of these antibody leads may be furthermutagenized in vitro or in vivo to generate secondary libraries withdiversity introduced in the context of the initial antibody leads. Themutagenized antibody leads can then be further screened for binding totarget antigens or biological activity, in vitro or in vivo, followingprocedures similar to those used for the selection of the initialantibody lead from the primary library. Such mutagenesis and selectionof primary antibody leads effectively mimics the affinity maturationprocess naturally occurring in a mammal that produces antibodies withprogressive increases in the affinity to an antigen. In one embodimentof the invention, only the CDRH3 region is mutagenized. In anotherembodiment of the invention, the whole variable region is mutagenized.In other embodiments of the invention one or more of CDRH1, CDRH2,CDRH3, CDRL1, CDRL2, and/ CDRL3 may be mutagenized. In some embodimentsof the invention, “light chain shuffling” may be used as part of theaffinity maturation protocol. In certain embodiments, this may involvepairing one or more heavy chains with a number of light chains, toselect light chains that enhance the affinity and/or biological activityof an antibody. In certain embodiments of the invention, the number oflight chains to which the one or more heavy chains can be paired is atleast about 2, 5, 10, 100, 1000, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, or 10¹⁰.In certain embodiments of the invention, these light chains are encodedby plasmids. In other embodiments of the invention, the light chains maybe integrated into the genome of the host cell.

The coding sequences of the antibody leads may be mutagenized by a widevariety of methods. Examples of methods of mutagenesis include, but arenot limited to site-directed mutagenesis, error-prone PCR mutagenesis,cassette mutagenesis, and random PCR mutagenesis. Alternatively,oligonucleotides encoding regions with the desired mutations can besynthesized and introduced into the sequence to be mutagenized, forexample, via recombination or ligation.

Site-directed mutagenesis or point mutagenesis may be used to graduallychange the CDR sequences in specific regions. This may be accomplishedby using oligonucleotide-directed mutagenesis or PCR. For example, ashort sequence of an antibody lead may be replaced with a syntheticallymutagenized oligonucleotide in either the heavy chain or light chainregion, or both. The method may not be efficient for mutagenizing largenumbers of CDR sequences, but may be used for fine tuning of aparticular lead to achieve higher affinity toward a specific targetprotein.

Cassette mutagenesis may also be used to mutagenize the CDR sequences inspecific regions. In a typical cassette mutagenesis, a sequence block,or a region, of a single template is replaced by a completely orpartially randomized sequence. However, the maximum information contentthat can be obtained may be statistically limited by the number ofrandom sequences of the oligonucleotides. Similar to point mutagenesis,this method may also be used for fine tuning of a particular lead toachieve higher affinity towards a specific target protein.

Error-prone PCR, or “poison” PCR, may be used to mutagenize the CDRsequences by following protocols described in Caldwell and Joyce, PCRMethods and Applications, 1992, 2: 28; Leung et al., Technique, 1989, 1:11; Shafikhani et al., Biotechniques, 1997, 23: 304; and Stemmer et al.,PNAS, 1994, 91: 10747 (each of which is incorporated by reference in itsentirety).

Conditions for error prone PCR may include (a) high concentrations ofMn²⁺ (e.g., about 0.4 to about 0.6 mM) that efficiently inducesmalfunction of Taq DNA polymerase; and (b) a disproportionally highconcentration of one nucleotide substrate (e.g., dGTP) in the PCRreaction that causes incorrect incorporation of this high concentrationsubstrate into the template and produces mutations. Additionally, otherfactors such as, the number of PCR cycles, the species of DNA polymeraseused, and the length of the template, may affect the rate ofmisincorporation of “wrong” nucleotides into the PCR product.Commercially available kits may be utilized for the mutagenesis of theselected antibody library, such as the “Diversity PCR random mutagenesiskit” (CLONTECH™).

The primer pairs used in PCR-based mutagenesis may, in certainembodiments, include regions matched with the homologous recombinationsites in the expression vectors. This design allows facilere-introduction of the PCR products back into the heavy or light chainchassis vectors, after mutagenesis, via homologous recombination.

Other PCR-based mutagenesis methods can also be used, alone or inconjunction with the error prone PCR described above. For example, thePCR amplified CDR segments may be digested with DNase to create nicks inthe double stranded DNA. These nicks can be expanded into gaps by otherexonucleases such as Bal 31. The gaps may then be filled by randomsequences by using DNA Klenow polymerase at a low concentration ofregular substrates dGTP, dATP, dTTP, and dCTP with one substrate (e.g.,dGTP) at a disproportionately high concentration. This fill-in reactionshould produce high frequency mutations in the filled gap regions. Thesemethod of DNase digestion may be used in conjunction with error pronePCR to create a high frequency of mutations in the desired CDR segments.

The CDR or antibody segments amplified from the primary antibody leadsmay also be mutagenized in vivo by exploiting the inherent ability ofmutation in pre-B cells. The Ig genes in pre-B cells are specificallysusceptible to a high-rate of mutation. The Ig promoter and enhancerfacilitate such high rate mutations in a pre-B cell environment whilethe pre-B cells proliferate. Accordingly, CDR gene segments may becloned into a mammalian expression vector that contains a human Igenhancer and promoter. This construct may be introduced into a pre-Bcell line, such as 38B9, which allows the mutation of the VH and VL genesegments naturally in the pre-B cells (Liu and Van Ness, Mol. Immunol.,1999, 36: 461, incorporated by reference in its entirety). Themutagenized CDR segments can be amplified from the cultured pre-B cellline and re-introduced back into the chassis-containing vectors) via,for example, homologous recombination.

In some embodiments, a CDR “hit” isolated from screening the library canbe re-synthesized, using degenerate codons or trinucleotides, andre-cloned into the heavy or light chain vector using gap repair.

3. LIBRARY SAMPLING

In certain embodiments of the invention, a library of the inventioncomprises a designed, non-random repertoire wherein the theoreticaldiversity of particular components of the library (for example, CDRH3),but not necessarily all components or the entire library, can beover-sampled in a physical realization of the library, at a level wherethere is a certain degree of statistical confidence (e.g., 95%) that anygiven member of the theoretical library is present in the physicalrealization of the library at least at a certain frequency (e.g., atleast once, twice, three times, four times, five times, or more) in thelibrary.

In a library, it is generally assumed that the number of copies of agiven clone obeys a Poisson probability distribution (see Feller, W. AnIntroduction to Probability Theory and Its Applications, 1968, Wiley NewYork, incorporated by reference in its entirety). The probability of aPoisson random number being zero, corresponding to the probability ofmissing a given component member in an instance of a library (seebelow), is e^(−N), where N is the average of the random number. Forexample, if there are 10⁶ possible theoretical members of a library anda physical realization of the library has 10⁷ members, with an equalprobability of each member of the theoretical library being sampled,then the average number of times that each member occurs in the physicalrealization of the library is 10⁷/10⁶=10, and the probability that thenumber of copies of a given member is zero is e^(−N)=e⁻¹⁰=0.000045; or a99.9955% chance that there is at least one copy of any of the 10⁶theoretical members in this 10× oversampled library. For a 2.3×oversampled library one is 90% confident that a given component ispresent. For a 3× oversampled library one is 95% confident that a givencomponent is present. For a 4.6× oversampled library one is 99%confident a given clone is present, and so on.

Therefore, if M is the maximum number of theoretical library membersthat can be feasibly physically realized, then M/3 is the maximumtheoretical repertoire size for which one can be 95% confident that anygiven member of the theoretical library will be sampled. It is importantto note that there is a difference between a 95% chance that a givenmember is represented and a 95% chance that every possible member isrepresented. In certain embodiments, the instant invention provides arationally designed library with diversity so that any given member is95% likely to be represented in a physical realization of the library.In other embodiments of the invention, the library is designed so thatany given member is at least about 0.0001%, 0.001%, 0.01%, 0.1%, 1%, 5%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 99%, 99.5%, or99.9% likely to be represented in a physical realization of the library.For a review, see, e.g., Firth and Patrick, Biomol. Eng., 2005, 22: 105,and Patrick et al., Protein Engineering, 2003, 16: 451, each of which isincorporated by reference in its entirety.

In certain embodiments of the invention, a library may have atheoretical total diversity of X unique members and the physicalrealization of the theoretical total diversity may contain at leastabout 1×, 2×, 3×, 4×, 5×, 6×, 7×, 8×9×, 10×, or more members. In someembodiments, the physical realization of the theoretical total diversitymay contain about 1× to about 2×, about 2× to about 3×, about 3× toabout 4×, about 4× to about 5×, about 5× to about 6× members. In otherembodiments, the physical realization of the theoretical total diversitymay contain about 1× to about 3×, or about 3× to about 5× total members.

An assumption underlying all directed evolution experiments is that theamount of molecular diversity theoretically possible is enormouscompared with the ability to synthesize it, physically realize it, andscreen it. The likelihood of finding a variant with improved propertiesin a given library is maximized when that library is maximally diverse.Patrick et al. used simple statistics to derive a series of equationsand computer algorithms for estimating the number of unique sequencevariants in libraries constructed by randomized oligonucleotidemutagenesis, error-prone PCR and in vitro recombination. They havewritten a suite of programs for calculating library statistics, such asGLUE, GLUE-IT, PEDEL, PEDEL-AA, and DRIVeR. These programs aredescribed, with instructions on how to access them, in Patrick et al.,Protein Engineering, 2003, 16: 451 and Firth et al., Nucleic Acids Res.,2008, 36: W281 (each of which is incorporated by reference in itsentirety).

It is possible to construct a physical realization of a library in whichsome components of the theoretical diversity (such as CDRH3) areoversampled, while other aspects (VH/VL pairings) are not. For example,consider a library in which 10⁸ CDRH3 segments are designed to bepresent in a single VH chassis, and then paired with 10⁵ VL genes toproduce 10¹³ (=10⁸*10⁵) possible full heterodimeric antibodies. If aphysical realization of this library is constructed with a diversity of10⁹ transformant clones, then the CDRH3 diversity is oversampledten-fold (=10⁹/10⁸), however the possible VH/VL pairings areundersampled by 10⁻⁴ (=10⁹/10¹³). In this example, on average, eachCDRH3 is paired only with 10 samples of the VL from the possible 10⁵partners. In certain embodiments of the invention, it is the CDRH3diversity that is preferably oversampled.

3.1. Other Variants of the Polynucleotide Sequences of the Invention

In certain embodiments, the invention relates to a polynucleotide thathybridizes with a polynucleotide taught herein, or that hybridizes withthe complement of a polynucleotide taught herein. For example, anisolated polynucleotide that remains hybridized after hybridization andwashing under low, medium, or high stringency conditions to apolynucleotide taught herein or the complement of a polynucleotidetaught herein is encompassed by the present invention.

Exemplary low stringency conditions include hybridization with a buffersolution of about 30% to about 35% formamide, about 1 M NaCl, about 1%SDS (sodium dodecyl sulphate) at about 37° C., and a wash in about 1× toabout 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at about 50° C.to about 55° C.

Exemplary moderate stringency conditions include hybridization in about40% to about 45% formamide, about 1 M NaCl, about 1% SDS at about 37°C., and a wash in about 0.5× to about 1× SSC at abut 55° C. to about 60°C.

Exemplary high stringency conditions include hybridization in about 50%formamide, about 1 M NaCl, about 1% SDS at about 37° C., and a wash inabout 0.1×SSC at about 60° C. to about 65° C.

Optionally, wash buffers may comprise about 0.1% to about 1% SDS.

The duration of hybridization is generally less than about 24 hours,usually about 4 to about 12 hours.

3.2. Sub-Libraries and Larger Libraries Comprising the Libraries orSub-Libraries of the Invention

As described throughout the application, the libraries of the currentinvention are distinguished, in certain embodiments, by their human-likesequence composition and length, and the ability to generate a physicalrealization of the library which contains all members of (or, in somecases, even oversamples) a particular component of the library.Libraries comprising combinations of the libraries described herein(e.g., CDRH3 and CDRL3 libraries) are encompassed by the invention.Sub-libraries comprising portions of the libraries described herein arealso encompassed by the invention (e.g., a CDRH3 library in a particularheavy chain chassis or a sub-set of the CDRH3 libraries). One ofordinary skill in the art will readily recognize that each of thelibraries described herein has several components (e.g., CDRH3, VH,CDRL3, VL, etc.), and that the diversity of these components can bevaried to produce sub-libraries that fall within the scope of theinvention.

Moreover, libraries containing one of the libraries or sub-libraries ofthe invention also fall within the scope of the invention. For example,in certain embodiments of the invention, one or more libraries orsub-libraries of the invention may be contained within a larger library,which may include sequences derived by other means, for example,non-human or human sequence derived by stochastic or semi-stochasticsynthesis. In certain embodiments of the invention, at least about 1% ofthe sequences in a polynucleotide library may be those of the invention(e.g., CDRH3 sequences, CDRL3 sequences, VH sequences, VL sequences),regardless of the composition of the other 99% of sequences. In otherembodiments of the invention, at least about 0.001%, 0.01%, 0.1%, 2%,5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91,%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%of the sequences in any polynucleotide library may be those of theinvention, regardless of the composition of the other sequences. In someembodiments, the sequences of the invention may comprise about 0.001% toabout 1%, about 1% to about 2%, about 2% to about 5%, about 5% to about10%, about 10% to about 15%, about 15% to about 20%, about 20% to about25%, about 25% to about 30%, about 30% to about 35%, about 35% to about40%, about 40% to about 45%, about 45% to about 50%, about 50% to about55%, about 55% to about 60%, about 60% to about 65%, about 65% to about70%, about 70% to about 75%, about 75% to about 80%, about 80% to about85%, about 85% to about 90%, about 90% to about 95%, or about 95% toabout 99% of the sequences in any polynucleotide library, regardless ofthe composition of the other sequences. Thus, libraries more diversethan one or more libraries or sub-libraries of the invention, but yetstill comprising one or more libraries or sub-libraries of theinvention, in an amount in which the one or more libraries orsub-libraries of the invention can be effectively screened and fromwhich sequences encoded by the one or more libraries or sub-libraries ofthe invention can be isolated, also fall within the scope of theinvention.

3.3. Alternative Scaffolds

In certain embodiments of the invention, the amino acid products of alibrary of the invention (e.g., a CDRH3 or CDRL3) may be displayed on analternative scaffold. Several of these scaffolds have been shown toyield molecules with specificities and affinities that rival those ofantibodies. Exemplary alternative scaffolds include those derived fromfibronectin (e.g., AdNectin), the β-sandwich (e.g., iMab), lipocalin(e.g., Anticalin), EETI-II/AGRP, BPTI/LACI-D1/ITI-D2 (e.g., Kunitzdomain), thioredoxin (e.g., peptide aptamer), protein A (e.g.,Affibody), ankyrin repeats (e.g., DARPin), γB-crystallin/ubiquitin(e.g., Affilin), CTLD₃ (e.g., Tetranectin), and (LDLR-A module)₃ (e.g.,Avimers). Additional information on alternative scaffolds are providedin Binz et al., Nat. Biotechnol., 2005 23: 1257 and Skerra, CurrentOpin. in Biotech., 2007 18: 295-304, each of which is incorporated byreference in its entirety.

4. OTHER EMBODIMENTS OF THE INVENTION

In certain embodiments, the invention comprises a synthetic preimmunehuman antibody CDRH3 library comprising 10⁷ to 10⁸ polynucleotidesequences representative of the sequence diversity and length diversityfound in known heavy chain CDR3 sequences.

In other embodiments, the invention comprises a synthetic preimmunehuman antibody CDRH3 library comprising polynucleotide sequencesencoding CDRH3 represented by the following formula:

[G/D/E/-][N1][DH][N2][H3-JH],

wherein [G/D/E/-] is zero to one amino acids in length, [N1] is zero tothree amino acids, [DH] is three to ten amino acids in length, [N2] iszero to three amino acids in length, and [H3-JH] is two to nine aminoacids in length.

In certain embodiments of the invention, [G/D/E/-] is represented by anamino acid sequence selected from the group consisting of: G, D, E, andnothing.

In some embodiments of the invention, [N1] is represented by an aminoacid sequence selected from the group consisting of: G, R, S, P, L, A,V, T, (G/P)(G/R/S/P/L/A/V/T), (R/S/L/A/V/T)(G/P), GG(G/R/S/P/L/A/V/T),G(R/S/P/L/A/V/T)G, (R/S/P/L/A/V/T)GG, and nothing.

In certain embodiments of the invention, [N2] is represented by an aminoacid sequence selected from the group consisting of: G, R, S, P, L, A,V, T, (G/P)(G/R/S/P/L/A/V/T), (R/S/L/A/V/T)(G/P), GG(G/R/S/P/L/A/V/T),G(R/S/P/L/A/V/T)G, (R/S/P/L/A/V/T)GG, and nothing.

In some embodiments of the invention, [DH] comprises a sequence selectedfrom the group consisting of: IGHD3-10 reading frame 1 (SEQ ID NO: 1),IGHD3-10 reading frame 2 (SEQ ID NO: 2), IGHD3-10 reading frame 3 (SEQID NO: 3), IGHD3-22 reading frame 2 (SEQ ID NO: 4), IGHD6-19 readingframe 1 (SEQ ID NO: 5), IGHD6-19 reading frame 2 (SEQ ID NO: 6),IGHD6-13 reading frame 1 (SEQ ID NO: 7), IGHD6-13 reading frame 2 (SEQID NO: 8), IGHD3-03 reading frame 3 (SEQ ID NO: 9), IGHD2-02 readingframe 2 (SEQ ID NO: 10), IGHD2-02 reading frame 3 (SEQ ID NO: 11),IGHD4-17 reading frame 2 (SEQ ID NO: 12), IGHD1-26 reading frame 1 (SEQID NO: 13), IGHD1-26 reading frame 3 (SEQ ID NO: 14), IGHD5-5/5-18reading frame 3 (SEQ ID NO: 15), IGHD2-15 reading frame 2 (SEQ ID NO:16), and all possible N-terminal and C-terminal truncations of theabove-identified IGHDs down to three amino acids.

In certain embodiments of the invention, [H3-JH] comprises a sequenceselected from the group consisting of: AEYFQH (SEQ ID NO: 17), EYFQH(SEQ ID NO: 583), YFQH (SEQ ID NO: 584), FQH, QH, YWYFDL (SEQ ID NO:18), WYFDL (SEQ ID NO: 585), YFDL (SEQ ID NO: 586), FDL, DL, AFDV (SEQID NO: 19), FDV, DV, YFDY (SEQ ID NO: 20), FDY, DY, NWFDS (SEQ ID NO:21), WFDS (SEQ ID NO: 586), FDS, DS, YYYYYGMDV (SEQ ID NO: 22), YYYYGMDV(SEQ ID NO: 587), YYYGMDV (SEQ ID NO: 588), YYGMDV (SEQ ID NO: 589),YGMDV (SEQ ID NO: 590), GMDV (SEQ ID NO: 591), MDV, and DV.

In some embodiments of the invention, the sequences represented by[G/D/E/-][N1][ext-DH][N2][H3-JH] comprise a sequence of about 3 to about26 amino acids in length.

In certain embodiments of the invention, the sequences represented by[G/D/E/-][N1][ext-DH][N2][H3-JH] comprise a sequence of about 7 to about23 amino acids in length.

In some embodiments of the invention, the library comprises about 10⁷ toabout 10¹⁰ sequences.

In certain embodiments of the invention, the library comprises about 10⁷sequences.

In some embodiments of the invention, the polynucleotide sequences ofthe libraries further comprise a 5′ polynucleotide sequence encoding aframework 3 (FRM3) region on the corresponding N-terminal end of thelibrary sequence, wherein the FRM3 region comprises a sequence of about1 to about 9 amino acid residues.

In certain embodiments of the invention, the FRM3 region comprises asequence selected from the group consisting of CAR, CAK, and CAT.

In some embodiments of the invention, the polynucleotide sequencesfurther comprise a 3′ polynucleotide sequence encoding a framework 4(FRM4) region on the corresponding C-terminal end of the librarysequence, wherein the FRM4 region comprises a sequence of about 1 toabout 9 amino acid residues.

In certain embodiments of the invention, the library comprises a FRM4region comprising a sequence selected from WGRG (SEQ ID NO: 23) and WGQG(SEQ ID NO: 23).

In some embodiments of the invention, the polynucleotide sequencesfurther comprise an FRM3 region coding for a corresponding polypeptidesequence comprising a sequence selected from the group consisting ofCAR, CAK, and CAT; and an FRM4 region coding for a correspondingpolypeptide sequence comprising a sequence selected from WGRG (SEQ IDNO: 23) and WGQG (SEQ ID NO: 23).

In certain embodiments of the invention, the polynucleotide sequencesfurther comprise 5′ and 3′ sequences which facilitate homologousrecombination with a heavy chain chassis.

In some embodiments, the invention comprises a synthetic preimmune humanantibody light chain library comprising polynucleotide sequencesencoding human antibody kappa light chains represented by the formula:

[IGKV(1-95)][F/L/I/R/W/Y][JK].

In certain embodiments of the invention, [IGKV (1-95)] is selected fromthe group consisting of IGKV3-20 (SEQ ID NO: 237) (1-95), IGKV1-39 (SEQID NO: 233) (1-95), IGKV3-11 (SEQ ID NO: 235) (1-95), IGKV3-15 (SEQ IDNO: 236) (1-95), IGKV1-05 (SEQ ID NO: 229) (1-95), IGKV4-01 (1-95),IGKV2-28 (SEQ ID NO: 234) (1-95), IGKV 1-33 (1-95), IGKV1-09 (SEQ ID NO:454) (1-95), IGKV1-12 (SEQ ID NO: 230) (1-95), IGKV2-30 (SEQ ID NO: 467)(1-95), IGKV1-27 (SEQ ID NO: 231) (1-95), IGKV1-16 (SEQ ID NO: 456)(1-95), and truncations of said group up to and including position 95according to Kabat.

In some embodiments of the invention, [F/L/I/R/W/Y] is an amino acidselected from the group consisting of F, L, I, R, W, and Y.

In certain embodiments of the invention, [JK] comprises a sequenceselected from the group consisting of TFGQGTKVEIK (SEQ ID NO: 528) andTFGGGT (SEQ ID NO: 529).

In some embodiments of the invention, the light chain library comprisesa kappa light chain library.

In certain embodiments of the invention, the polynucleotide sequencesfurther comprise 5′ and 3′ sequences which facilitate homologousrecombination with a light chain chassis.

In some embodiments, the invention comprises a method for producing asynthetic preimmune human antibody CDRH3 library comprising 10⁷ to 10⁸polynucleotide sequences, said method comprising:

-   -   a) selecting the CDRH3 polynucleotide sequences encoded by the        CDRH3 sequences, as follows:        -   {0 to 5 amino acids selected from the group consisting of            fewer than ten of the amino acids preferentially encoded by            terminal deoxynucleotidyl transferase (TdT) and            preferentially functionally expressed by human B cells},            followed by        -   {all possible N or C-terminal truncations of IGHD alone and            all possible combinations of N and C-terminal truncations},            followed by        -   {0 to 5 amino acids selected from the group consisting of            fewer than ten of the amino acids preferentially encoded by            TdT and preferentially functionally expressed by human B            cells}, followed by        -   {all possible N-terminal truncations of IGHJ, down to DXWG,            wherein X is S, V, L, or Y}; and    -   b) synthesizing the CDRH3 library described in a) by chemical        synthesis, wherein a synthetic preimmune human antibody CDRH3        library is produced.

In certain embodiments, the invention comprises a synthetic preimmunehuman antibody CDRH3 library comprising 10⁷ to 10¹⁰ polynucleotidesequences representative of known human IGHD and IGHJ germline sequencesencoding CDRH3, represented by the following formula:

-   -   {0 to 5 amino acids selected from the group consisting of fewer        than ten of the amino acids preferentially encoded by terminal        deoxynucleotidyl transferase (TdT) and preferentially        functionally expressed by human B cells}, followed by {all        possible N or C-terminal truncations of IGHD alone and all        possible combinations of N and C-terminal truncations}, followed        by    -   {0 to 5 amino acids selected from the group consisting of fewer        than ten of the amino acids preferentially encoded by TdT and        preferentially functionally expressed by human B cells},        followed by    -   {all possible N-terminal truncations of IGHJ, down to DXWG (SEQ        ID NO: 530), wherein X is S, V, L, or Y}.

In certain embodiments, the invention comprises a synthetic preimmunehuman antibody heavy chain variable domain library comprising 10⁷ to10¹⁰ polynucleotide sequences encoding human antibody heavy chainvariable domains, said library comprising:

-   -   a) an antibody heavy chain chassis, and    -   b) a CDRH3 repertoire designed based on the human IGHD and IGHJ        germline sequences, as follows:        -   {0 to 5 amino acids selected from the group consisting of            fewer than ten of the amino acids preferentially encoded by            terminal deoxynucleotidyl transferase (TdT) and            preferentially functionally expressed by human B cells},            followed by        -   {all possible N or C-terminal truncations of IGHD alone and            all possible combinations of N and C-terminal truncations},            followed by        -   {0 to 5 amino acids selected from the group consisting of            fewer than ten of the amino acids preferentially encoded by            TdT and preferentially functionally expressed by human B            cells}, followed by        -   {all possible N-terminal truncations of IGHJ, down to DXWG            (SEQ ID NO: 530), wherein X is S, V, L, or Y}.

In some embodiments of the invention, the synthetic preimmune humanantibody heavy chain variable domain library is expressed as a fulllength chain selected from the group consisting of an IgG1 full lengthchain, an IgG2 full length chain, an IgG3 full length chain, and an IgG4full length chain.

In certain embodiments of the invention, the human antibody heavy chainchassis is selected from the group consisting of IGHV4-34 (SEQ ID NO:35), IGHV3-23 (SEQ ID NO: 30), IGHV5-51 (SEQ ID NO: 40), IGHV1-69 (SEQID NO: 27), IGHV3-30 (SEQ ID NO: 31), IGHV4-39 (SEQ ID NO: 36), IGHV1-2(SEQ ID NO: 24), IGHV1-18 (SEQ ID NO: 25), IGHV2-5 (SEQ ID NO: 429),IGHV2-70 (SEQ ID NO: 431, 432), IGHV3-7 (SEQ ID NO: 28), IGHV6-1 (SEQ IDNO: 449), IGHV1-46 (SEQ ID NO: 26), IGHV3-33 (SEQ ID NO: 32), IGHV4-31(SEQ ID NO: 34), IGHV4-4 (SEQ ID NO: 446, 447), IGHV4-61 (SEQ ID NO:38), and IGHV3-15 (SEQ ID NO: 29).

In some embodiments of the invention, the synthetic preimmune humanantibody heavy chain variable domain library comprises 10⁷ to 10¹⁰polynucleotide sequences encoding human antibody heavy chain variabledomains, said library comprising:

-   -   a) an antibody heavy chain chassis, and    -   b) a synthetic preimmune human antibody CDRH3 library.

In some embodiments of the invention, the polynucleotide sequences aresingle-stranded coding polynucleotide sequences.

In certain embodiments of the invention, the polynucleotide sequencesare single-stranded non-coding polynucleotide sequences.

In some embodiments of the invention, the polynucleotide sequences aredouble-stranded polynucleotide sequences.

In certain embodiments, the invention comprises a population ofreplicable cells with a doubling time of four hours or less, in which asynthetic preimmune human antibody repertoire is expressed.

In some embodiments of the invention, the population of replicable cellsare yeast cells.

In certain embodiments, the invention comprises a method of generating afull-length antibody library comprising transforming a cell with apreimmune human antibody heavy chain variable domain library and asynthetic preimmune human antibody light chain library.

In some embodiments, the invention comprises a method of generating afull-length antibody library comprising transforming a cell with apreimmune human antibody heavy chain variable domain library and asynthetic preimmune human antibody light chain library.

In certain embodiments, the invention comprises a method of generatingan antibody library comprising synthesizing polynucleotide sequences bysplit-pool DNA synthesis.

In some embodiments of the invention, the polynucleotide sequences areselected from the group consisting of single-stranded codingpolynucleotide sequences, single-stranded non-coding polynucleotidesequences, and double-stranded polynucleotide sequences.

In certain embodiments, the invention comprises a synthetic full-lengthpreimmune human antibody library comprising about 10⁷ to about 10¹⁰polynucleotide sequences representative of the sequence diversity andlength diversity found in known heavy chain CDR3 sequences.

In certain embodiments, the invention comprises a method of selecting anantibody of interest from a human antibody library, comprising providinga synthetic preimmune human antibody CDRH3 library comprising atheoretical diversity of (N) polynucleotide sequences representative ofthe sequence diversity and length diversity found in known heavy chainCDR3 sequences, wherein the physical realization of that diversity is anactual library of a size at least 3(N), thereby providing a 95%probability that a single antibody of interest is present in thelibrary, and selecting an antibody of interest.

In some embodiments of the invention, the theoretical diversity is about10⁷ to about 10⁸ polynucleotide sequences.

EXAMPLES

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references,patents and published patent applications cited throughout thisapplication are hereby incorporated by reference.

In general, the practice of the present invention employs, unlessotherwise indicated, conventional techniques of chemistry, molecularbiology, recombinant DNA technology, PCR technology, immunology(especially, e.g., antibody technology), expression systems (e.g., yeastexpression, cell-free expression, phage display, ribosome display, andPROFUSION™), and any necessary cell culture that are within the skill ofthe art and are explained in the literature. See, e.g., Sambrook,Fritsch and Maniatis, Molecular Cloning: Cold Spring Harbor LaboratoryPress (1989); DNA Cloning, Vols. 1 and 2, (D. N. Glover, Ed. 1985);Oligonucleotide Synthesis (M. J. Gait, Ed. 1984); PCR Handbook CurrentProtocols in Nucleic Acid Chemistry, Beaucage, Ed. John Wiley & Sons(1999) (Editor); Oxford Handbook of Nucleic Acid Structure, Neidle, Ed.,Oxford Univ Press (1999); PCR Protocols: A Guide to Methods andApplications, Innis et al., Academic Press (1990); PCR EssentialTechniques: Essential Techniques, Burke, Ed., John Wiley & Son Ltd(1996); The PCR Technique: RT-PCR, Siebert, Ed., Eaton Pub. Co. (1998);Antibody Engineering Protocols (Methods in Molecular Biology), 510,Paul, S., Humana Pr (1996); Antibody Engineering: A Practical Approach(Practical Approach Series, 169), McCafferty, Ed., Irl Pr (1996);Antibodies: A Laboratory Manual, Harlow et al., C.S.H.L. Press, Pub.(1999); Current Protocols in Molecular Biology, eds. Ausubel et al.,John Wiley & Sons (1992); Large-Scale Mammalian Cell Culture Technology,Lubiniecki, A., Ed., Marcel Dekker, Pub., (1990); Phage Display: ALaboratory Manual, C. Barbas (Ed.), CSHL Press, (2001); Antibody PhageDisplay, P O'Brien (Ed.), Humana Press (2001); Border et al., NatureBiotechnology, 1997, 15: 553; Border et al., Methods Enzymol., 2000,328: 430; ribosome display as described by Pluckthun et al. in U.S. Pat.No. 6,348,315, and Profusion™ as described by Szostak et al. in U.S.Pat. Nos. 6,258,558; 6,261,804; and 6,214,553; and bacterial periplasmicexpression as described in US20040058403A1. Each of the references citedin this paragraph is incorporated by reference in its entirety.

Further details regarding antibody sequence analysis using Kabatconventions and programs to screen aligned nucleotide and amino acidsequences may be found, e.g., in Johnson et al., Methods Mol. Biol.,2004, 248: 11; Johnson et al., Int. Immunol., 1998, 10: 1801; Johnson etal., Methods Mol. Biol., 1995, 51: 1; Wu et al., Proteins, 1993, 16: 1;and Martin, Proteins, 1996, 25: 130. Each of the references cited inthis paragraph is incorporated by reference in its entirety.

Further details regarding antibody sequence analysis using Chothiaconventions may be found, e.g., in Chothia et al., J. Mol. Biol., 1998,278: 457; Morea et al., Biophys. Chem., 1997, 68: 9; Morea et al., J.Mol. Biol., 1998, 275: 269; Al-Lazikani et al., J. Mol. Biol., 1997,273: 927. Barre et al., Nat. Struct. Biol., 1994, 1: 915; Chothia etal., J. Mol. Biol., 1992, 227: 799; Chothia et al., Nature, 1989, 342:877; and Chothia et al., J. Mol. Biol., 1987, 196: 901. Further analysisof CDRH3 conformation may be found in Shirai et al., FEBS Lett., 1999,455: 188 and Shirai et al., FEBS Lett., 1996, 399: 1. Further detailsregarding Chothia analysis are described, for example, in Chothia etal., Cold Spring Harb. Symp. Quant Biol., 1987, 52: 399. Each of thereferences cited in this paragraph is incorporated by reference in itsentirety.

Further details regarding CDR contact considerations are described, forexample, in MacCallum et al., J. Mol. Biol., 1996, 262: 732,incorporated by reference in its entirety.

Further details regarding the antibody sequences and databases referredto herein are found, e.g., in Tomlinson et al., J. Mol. Biol., 1992,227: 776, VBASE2 (Retter et al., Nucleic Acids Res., 2005, 33: D671);BLAST (www.ncbi.nlm.nih.gov/BLAST/); CDHIT(bioinformatics.ljcrf.edu/cd-hi/); EMBOSS(www.hgmp.mrc.ac.uk/Software/EMBOSS/); PHYLIP(evolution.genetics.washington.edu/phylip.html); and FASTA(fasta.bioch.virginia.edu). Each of the references cited in thisparagraph is incorporated by reference in its entirety.

Example 1 Design of an Exemplary VH Chassis Library

This example demonstrates the selection and design of exemplary,non-limiting VH chassis sequences of the invention. VH chassis sequenceswere selected by examining collections of human IGHV germline sequences(Scaviner et al., Exp. Clin. Immunogenet., 1999, 16: 234; Tomlinson etal., J. Mol. Biol., 1992, 227: 799; Matsuda et al., J. Exp. Med., 1998,188: 2151, each incorporated by reference in its entirety). As discussedin the Detailed Description, as well as below, a variety of criteria canbe used to select VH chassis sequences, from these data sources orothers, for inclusion in the library.

Table 3 (adapted from information provided in Scaviner et al., Exp.Clin. Immunogenet., 1999, 16: 234; Matsuda et cd., J. Exp. Med., 1998,188: 2151; and Wang et al. Immunol. Cell. Biol., 2008, 86: 111, eachincorporated by reference in its entirety) lists the CDRH1 and CDRH2length, the canonical structure and the estimated relative occurrence inperipheral blood, for the proteins encoded by each of the human IGHVgermline sequences.

TABLE 3 IGHV Characteristics and Occurrence in Antibodies fromPeripheral Blood Estimated Relative IGHV Length of Length of CanonicalOccurrence in Germline CDRH1 CDRH2 Structures¹ Peripheral Blood² IGHV1-25 17 1-3 37 IGHV1-3 5 17 1-3 15 IGHV1-8 5 17 1-3 13 IGHV1-18 5 17 1-2 25IGHV1-24 5 17 1-U 5 IGHV1-45 5 17 1-3 0 IGHV1-46 5 17 1-3 25 IGHV1-58 517 1-3 2 IGHV1-69 5 17 1-2 58 IGHV2-5 7 16 3-1 10 IGHV2-26 7 16 3-1 9IGHV2-70 7 16 3-1 13 IGHV3-7 5 17 1-3 26 IGHV3-9 5 17 1-3 15 IGHV3-11 517 1-3 13 IGHV3-13 5 16 1-1 3 IGHV3-15 5 19 1-4 14 IGHV3-20 5 17 1-3 3IGHV3-21 5 17 1-3 19 IGHV3-23 5 17 1-3 80 IGHV3-30 5 17 1-3 67 IGHV3-335 17 1-3 28 IGHV3-43 5 17 1-3 2 IGHV3-48 5 17 1-3 21 IGHV3-49 5 19 1-U 8IGHV3-53 5 16 1-1 7 IGHV3-64 5 17 1-3 2 IGHV3-66 5 17 1-3 3 IGHV3-72 519 1-4 2 IGHV3-73 5 19 1-4 3 IGHV3-74 5 17 1-3 14 IGHV4-4 5 16 1-1 33IGHV4-28 6 16 2-1 1 IGHV4-31 7 16 3-1 25 IGHV4-34 5 16 1-1 125 IGHV4-397 16 3-1 63 IGHV4-59 5 16 1-1 51 IGHV4-61 7 16 3-1 23 IGHV4-B 6 16 2-1 7IGHV5-51 5 17 1-2 52 IGHV6-1 7 18 3-5 26 IGHV7-4-1 5 17 1-2 8 ¹Adaptedfrom Chothia et al., J. Mol. Biol., 1992, 227: 799 ²Adapted from TableS1 of Wang et al., Immunol. Cell. Biol., 2008, 86: 111

In the currently exemplified library, 17 germline sequences were chosenfor representation in the VH chassis of the library (Table 4). Asdescribed in more detail below, these sequences were selected based ontheir relatively high representation in the peripheral blood of adults,with consideration given to the structural diversity of the chassis andthe representation of particular germline sequences in antibodies usedin the clinic. These 17 sequences account for about 76% of the totalsample of heavy chain sequences used to derive the results of Table 4.As outlined in the Detailed Description, these criteria arenon-limiting, and one of ordinary skill in the art will readilyrecognize that a variety of other criteria can be used to select the VHchassis sequences, and that the invention is not limited to a librarycomprising the 17 VH chassis genes presented in Table 4.

TABLE 4 VH Chassis Selected for Use in the Exemplary Library RelativeLength of Length of VH Chassis Occurrence CDRH1 CDRH2 Comment VH1-2 37 517 Among highest usage for VH1 family VH1-18 25 5 17 Among highest usagefor VH1 family VH1-46 25 5 17 Among highest usage for VH1 family VH1-6958 5 17 Highest usage for VH1 family. The four chosen VH1 chassisrepresent about 80% of the VH1 repertoire. VH3-7 26 5 17 Among highestusage in VH3 family VH3-15 14 5 19 Not among highest usage, but it hasunique structure (H2 of length 19). Highest occurrence among those withsuch structure. VH3-23 80 5 17 Highest usage in VH3 family. VH3-30 67 517 Among highest usage in VH3 family VH3-33 28 5 17 Among highest usagein VH3 family VH3-48 21 5 17 Among highest usage in VH3 family. The sixchosen VH3 chassis account for about 70% of the VH3 repertoire. VH4-3125 7 16 Among highest usage in VH4 family VH4-34 125 5 16 Highest usagein VH4 family VH4-39 63 7 16 Among highest usage in VH4 family VH4-59 515 16 Among highest usage in VH4 family VH4-61 23 7 16 Among highestusage in VH4 family VH4-B 7 6 16 Not among highest usage in VH4 family,but has unique structure (H1 of length 6). The 6 chosen VH4 chassisaccount for close to 90% of the VH4 family repertoire VH5-51 52 5 17High usage

In this particular embodiment of the library, VH chassis derived fromsequences in the IGHV2, IGHV6 and IGHV7 germline families were notincluded. As described in the Detailed Description, this exemplificationis not meant to be limiting, as, in some embodiments, it may bedesirable to include one or more of these families, particularly asclinical information on antibodies with similar sequences becomesavailable, to produce libraries with additional diversity that ispotentially unexplored, or to study the properties and potential ofthese IGHV families in greater detail. The modular design of the libraryof the present invention readily permits the introduction of these, andother, VH chassis sequences. The amino acid sequences of the VH chassisutilized in this particular embodiment of the library, which are derivedfrom the IGHV germline sequences, are presented in Table 5. The detailsof the derivation procedures are presented below.

TABLE 5 Amino Acid Sequences for VH Chassis Selectedfor Inclusion in the Exemplary Library SEQ ID Chassis NO: FRM1 CDRH1FRM2 CDRH2 FRM3 VH1-2 24 QVQLVQSG GYYMH WVRQAPG WINPNSG RVTMTRDTSIAEVKKPGA QGLEWMG GTNYAQK STAYMELSRL SVKVSCKA FQG RSDDTAVYYC SGYTFT ARVH1-18 25 QVQLVQSG SYGIS WVRQAPG WISAYNG RVTMTTDTST AEVKKPGA QGLEWMGNTNYAQK STAYMELRSL SVKVSCKA LQG RSDDTAVYYC SGYTFT AR VH1-46 26 QVQLVQSGSYYMH WVRQAPG IINPSGG RVTMTRDTST AEVKKPGA QGLEWMG STSYAQK STVYMELSSLSVKVSCKA FQG RSEDTAVYYC SGYTFT AR VH1-69 27 QVQLVQSG SYAIS WVRQAPGGIIPIFG RVTITADKST AEVKKPGS QGLEWMG TANYAQK STAYMELSSL SVKVSCKA FQGRSEDTAVYYC SGGTFS AR VH3-7 28 EVQLVESG SYWMS WVRQAPG NIKQDGS RFTISRDNAKGGLVQPGG KGLEWVA EKYYVDS NSLYLQMNSL SLRLSCAA VKG RAEDTAVYYC SGFTFS ARVH3-15¹ 29 EVQLVESG NAWMS WVRQAPG RIKSKTD RFTISRDDSK GGLVKPGG KGLEWVGGGTTDYA NTLYLQMNSL SLRLSCAA APVKG RA EDTAVYYC SGFTFS AR VH3-23 30EVQLLESG SYAMS WVRQAPG AISGSGG RFTISRDNSK GGLVQPGG KGLEWVS STYYADSNTLYLQMNSL SLRLSCAA VKG RAEDTAVYYC SGFTFS AK VH3-30 31 QVQLVESG SYGMHWVRQAPG VISYDGS RFTISRDNSK GGVVQPGR KGLEWVA NKYYADS NTLYLQMNSL SLRLSCAAVKG RAEDTAVYYC SGFTFS AR VH3-33 32 QVQLVESG SYGMH WVRQAPG VIWYDGSRFTISRDNSK GGVVQPGR KGLEWVA NKYYADS NTLYLQMNSL SLRLSCAA VKG RAEDTAVYYCSGFTFS AR VH3-48 33 EVQLVESG SYSMN WVRQAPG YISSSSS RFTISRDNAK GGLVQPGGKGLEWVS TIYYADS NSLYLQMNSL SLRLSCAA VKG RAEDTAVYYC SGFTFS AR VH4-31 34QVQLQESG  SGGYY  WIRQHPG YIYYSGS  RVTISVDTSK PGLVKPSQ  WS KGLEWIG TYYNPSL NQFSLKLSSV TLSLTCTV KS TAADTAVYYC SGGSIS AR VH4-34² 35 QVQLQQWG GYYWS  WIRQPPG  EI DHS GS RVTISVDTSK AGLLKPSE KGLEWIG TNYNPSL NQFSLKLSSV TLSLTCAV KS TAADTAVYYC YGGSFS AR VH4-39 36 QLQLQESG  SSSYY WIRQPPG SIYYSGS  RVTISVDTSK PGLVKPSE  WG KGLEWIG TYYNPSL  NQFSLKLSSVTLSLTCTV KS TAADTAVYYC SGGSIS AR VH4-59 37 QVQLQESG  SYYWS  WIRQPPG YIYYSGS RVTISVDTSK PGLVKPSE KGLEWIG TNYNPSL  NQFSLKLSSV TLSLTCTV KSTAADTAVYYC SGGSIS AR VH4-61 38 QVQLQESG  SGSYY  WIRQPPG  YIYYSGSRVTISVDTSK PGLVKPSE  WS KGLEWIG TNYNPSL  NQFSLKLSSV TLSLTCTV KSTAADTAVYYC SGGSVS AR VH4-B 39 QVQLQESG  SGYYW  WIRQPPG SIYHSGS RVTISVDTSK PGLVKPSE  G KGLEWIG TYYNPSL  NQFSLKLSSV TLSLTCAV KSTAADTAVYYC SGYSIS AR VH5-51 40 EVQLVQSG  SYWIG  WVRQMPG IIYPGDS QVTISADKSI AEVKKPGE KGLEWMG DTRYSPS  STAYLQWSSL SLKISCKG FQG KASDTAVYYCSGYSFT AR ¹The original KT sequence in VH3-15 was mutated to RA(bold/underlined) and TT to AR (bold/underlined), in order to matchother VH3 family members selected for inclusion in the library. Themodification to RA was made so that no unique sequence stretches of upto about 20 amino acids are created. Without being bound by theory, thismodification is expected to reduce the odds of introducing novel T-cellepitopes in the VH3-15-derived chassis sequence. The avoidance of T cellepitopes is an additional criterion that can be considered in the designof certain libraries of the invention. ²The original NHS motif in VH4-34was mutated to DHS, in order to remove a possible N-linked glycosylationsite in CDR-H2. In certain embodiments of the invention, for example, ifthe library is transformed into yeast, this may prevent unwantedN-linked glycosylation.

Table 5 provides the amino acid sequences of the seventeen chassis. Innucleotide space, most of the corresponding germline nucleotidesequences include two additional nucleotides on the 3′ end (i.e.,two-thirds of a codon). In most cases, those two nucleotides are GA. Inmany cases, nucleotides are added to the 3′ end of the IGHV-derived genesegment in vivo, prior to recombination with the IGHD gene segment. Anyadditional nucleotide would make the resulting codon encode one of thefollowing two amino acids: Asp (if the codon is GAC or GAT) or Glu (ifthe codon is GAA or GAG). One, or both, of the two 3′-terminalnucleotides may also be deleted in the final rearranged heavy chainsequence. If only the A is deleted, the resulting amino acid is veryfrequently a G. If both nucleotides are deleted, this position is“empty,” but followed by a general V-D addition or an amino acid encodedby the IGHD gene. Further details are presented in Example 5. This firstposition, after the CAR or CAK motif at the C-terminus of FRM3 (Table5), is designated the “tail.” In the currently exemplified embodiment ofthe library, this residue may be G, D, E, or nothing. Thus, adding thetail to any chassis enumerated above (Table 5) can produce one of thefollowing four schematic sequences, wherein the residue following the VHchassis is the tail:

-   -   (1) [VH_Chassis]-[G]    -   (2) [VH_Chassis]-[D]    -   (3) [VH_Chassis]-[E]    -   (4) [VH_Chassis]

These structures can also be represented in the format:

[VH_Chassis]-[G/D/E/-],

wherein the hyphen symbol (−) indicates an empty or null position.

Using the CDRH3 numbering system defined in the Definitions section, theabove sequences could be denoted to have amino acid 95 as G, D, or E,for instances (1), (2), and (3), respectively, while the sequence ofinstance 4 would have no position 95, and CDRH3 proper would begin atposition 96 or 97.

In some embodiments of the invention, VH3-66, with canonical structure1-1 (five residues in CDRH1 and 16 for CDRH2) may be included in thelibrary. The inclusion of VH3-66 may compensate for the removal of otherchassis from the library, which may not express well in yeast under someconditions (e.g., VH4-34 and VH4-59).

Example 2 Design of VH Chassis Variants with Variation within CDRH1 andCDRH2

This example demonstrates the introduction of further diversity into theVH chassis by creating mutations in the CDRH1 and CDRH2 regions of eachchassis shown in Example 1. The following approach was used to selectthe positions and nature of the amino acid variation for each chassis:First, the sequence identity between rearranged human heavy chainantibody sequences was analyzed (Lee et al., Immunogenetics, 2006, 57:917; Jackson et al., J. Immunol. Methods, 2007, 324: 26) and they wereclassified by the origin of their respective IGHV germline sequence. Asan illustrative example, about 200 sequences in the data set exhibitedgreatest identity to the IGHV1-69 germline, indicating that they werelikely to have been derived from IGHV1-69. Next, the occurrence of aminoacid residues at each position within the CDRH1 and CDRH2 segments, ineach germline family selected in Example 1 was determined. For VH1-69,these occurrences are illustrated in Tables 6 and 7. Second, neutraland/or smaller amino acid residues were favored, where possible, asreplacements. Without being bound by theory, the rationale for thechoice of these amino acid residues is the desire to provide a moreflexible and less sterically hindered context for the display of adiversity of CDR sequences.

TABLE 6 Occurrence of Amino Acid Residues at Each Position WithinIGHV1-69-derived CDRH1 Sequences 31 32 33 34 35 S Y A I S A 1 0 129  0 0C 0 1 0 0 2 D 0 5 1 0 0 E 0 0 0 0 0 F 0 9 1 8 0 G 0 0 24  0 3 H 2 11  00 4 I 2 0 0 159  1 K 3 0 0 0 0 L 0 10  2 5 0 M 1 0 0 0 0 N 21  2 2 0 27 P 0 0 1 0 0 Q 1 1 0 0 5 R 9 0 0 0 1 S 133  3 7 0 129  T 12  1 10  0 12 V 0 0 7 13  0 W 0 0 0 0 0 Y 0 142  1 0 1

TABLE 7 Occurrence of Amino Acid Residues at Each Position WithinIGHV1-69-derived CDRH2 Sequences 50 51 52 52A 53 54 55 56 57 58 59 60 6162 63 64 65 G I I P I F G T A N Y A Q K F Q G A 0 0 7 0 2 0 4 3 132 0 0178 0 0 0 0 0 C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 D 1 0 0 0 0 0 11 0 121 0 0 0 2 0 0 12 E 2 0 0 0 0 0 4 0 0 2 0 1 1 4 0 2 0 F 0 1 0 1 7 119 00 0 0 0 0 0 0 180 0 0 G 135 0 1 0 0 0 155 0 3 1 0 0 0 0 0 0 173 H 0 0 00 1 0 0 0 0 4 4 0 3 0 0 4 0 I 0 166 159 0 132 2 0 34 0 2 1 0 0 0 0 0 0 K1 0 0 0 0 0 0 4 1 5 0 0 2 156 0 3 0 L 0 1 2 0 16 37 0 1 0 0 0 0 0 0 3 20 M 0 6 2 0 9 1 0 3 1 0 0 0 0 0 0 0 0 N 0 0 1 0 2 0 5 0 0 132 1 0 0 8 00 0 P 0 2 0 181 1 3 0 0 15 0 0 3 6 0 0 0 0 Q 0 0 0 0 0 0 1 0 1 0 0 0 1732 0 164 0 R 44 0 0 0 0 0 1 4 0 3 0 0 0 13 0 9 0 S 1 0 1 1 2 6 3 5 8 7 02 0 0 1 0 0 T 1 1 7 2 2 1 0 127 15 8 3 1 0 0 0 0 0 V 0 8 5 0 11 4 0 4 80 0 0 0 0 0 0 0 W 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 Y 0 0 0 0 0 11 1 0 00 176 0 0 0 1 1 0

The original germline sequence is provided in the second row of thetables, in bold font, beneath the residue number (Kabat system). Theentries in the table indicate the number of times a given amino acidresidue (first column) is observed at the indicated CDRH1 (Table 6) orCDRH2 (Table 7) position. For example, at position 33 the amino acidtype G (glycine) is observed 24 times in the set of IGHV1-69-basedsequences that were examined. Thus, applying the criteria above,variants were constructed with N at position 31, L at position 32 (H canbe charged, under some conditions), G and T at position 33, no variantsat position 34 and N at position 35, resulting in the following VH1-69chassis CDRH1 single-amino acid variant sequences:

(SEQ ID NO: 41) N YAIS (SEQ ID NO: 42) S L AIS (SEQ ID NO: 43) SY G IS(SEQ ID NO: 44) SY T IS (SEQ ID NO: 45) SYAI N

Similarly, the analysis that produced Table 7 provided a basis forchoosing the following single-amino acid variant sequences for VH1-69chassis CDRH2s:

(SEQ ID NO: 46) S IIPIFGTANYAQKFQG (SEQ ID NO: 47) GI A PIFGTANYAQKFQG(SEQ ID NO: 48) GIIPI L GTANYAQKFQG (SEQ ID NO: 49) GIIPIFGTA S YAQKFQG

A similar approach was used to design and construct variants of theother selected chassis; the resulting CDRH1 and CDRH2 variants for eachof the exemplary chassis are provided in Table 8. One of ordinary skillin the art will readily recognize that the methods described herein canbe applied to create variants of other VH chassis and VL chassis.

TABLE 8 VH Chassis Variants SEQ SEQ SEQ SEQ ID ID ID ID Chassis CDRH1NO: CDRH2 NO: Chassis CDRH1 NO: CDRH2 NO: 1-18.0 SYGIS 50 WISAYNGNT 563-48.0  SYSMN 129 YISSSSSTI 136 NYAQKLQG YYADSVKG 1-18.1 N YGIS 51WISAYNGNT 56 3-48.1¹ N YSMN 130 YISSSSSTI 136 NYAQKLQG YYADSVKG 1-18.2 SN GIS 52 WISAYNGNT 56 3-48.2  I YSMN 131 YISSSSSTI 136 NYAQKLQG YYADSVKG1-18.3 SY A IS 53 WISAYNGNT 56 3-48.3  S N SMN 132 YISSSSSTI 136NYAQKLQG YYADSVKG 1-18.4 SYGI T 54 WISAYNGNT 56 3-48.4  SY E MN 133YISSSSSTI 136 NYAQKLQG YYADSVKG 1-18.5 SYGI H 55 WISAYNGNT 56 3-48.5  SYN MN 134 YISSSSSTI 136 NYAQKLQG YYADSVKG 1-18.6 SYGIS 50 S ISAYNGNT 573-48.6  SYSM T 135 YISSSSSTI 136 NYAQKLQG YYADSVKG 1-18.7 SYGIS 50 WIS TYNGNT 58 3-48.7  SYSMN 129 TISSSSSTI 137 NYAQKLQG YYADSVKG 1-18.8 SYGIS50 WIS P YNGNT 59 3-48.8  SYSMN 129 YISGSSSTI 138 NYAQKLQG YYADSVKG1-18.9 SYGIS 50 WIS A YNGNT 60 3-48.9  SYSMN 129 YISSSSSTI 139 YYAQKLQGL YADSVKG 1-2.0 GYYMH 61 WINPNSGGT 67 3-7.0  SYWMS 140 NIKQDGSEK 152NYAQKFQG YYVDSVKG 1-2.1 D YYMH 62 WINPNSGGT 67 3-7.1  T YWMS 141NIKQDGSEK 152 NYAQKFQG YYVDSVKG 1-2.2 R YYMH 63 WINPNSGGT 67 3-7.2  NYWMS 142 NIKQDGSEK 152 NYAQKFQG YYVDSVKG 1-2.3 G S YMH 64 WINPNSGGT 673-7.3  S S WMS 143 NIKQDGSEK 152 NYAQKFQG YYVDSVKG 1-2.4 GY S MH 65WINPNSGGT 67 3-7.4  SY G MS 144 NIKQDGSEK 152 NYAQKFQG YYVDSVKG 1-2.5GYYM Q 66 WINPNSGGT 67 3-7.5  SYWM T 145 NIKQDGSEK 152 NYAQKFQG YYVDSVKG1-2.6 GYYMH 61 S INPNSGGT 68 3-7.6  SYWMS 140 S IKQDGSEK 153 NYAQKFQGYYVDSVKG 1-2.7 GYYMH 61 WINP S SGGT 69 3-7.7  SYWMS 140 NI N QDGSEK 154NYAQKFQG YYVDSVKG 1-2.8 GYYMH 61 WINPNSGGT 70 3-7.8  SYWMS 140 NIK SDGSEK 155 K YAQKFQG YYVDSVKG 1-2.9 GYYMH 61 WINPNSGGT 71 3-7.9  SYWMS140 NIKQDGSEK 156 S YAQKFQG Q YVDSVKG 1-46.0 SYYMH 72 IINPSGGST 794-31.0 SGGYYWS 147 YIYYSGSTY 157 SYAQKFQG YNPSLKS 1-46.1 N YYMH 73IINPSGGST 79 4-31.1 SG S YYWS 148 YIYYSGSTY 157 SYAQKFQG YNPSLKS 1-46.2S S YMH 74 IINPSGGST 79 4-31.2 SG T YYWS 149 YIYYSGSTY 157 SYAQKFQGYNPSLKS 1-46.3 SY S MH 75 IINPSGGST 79 4-31.3 SGG T YWS 150 YIYYSGSTY157 SYAQKFQG YNPSLKS 1-46.4 SYY I H 76 IINPSGGST 79 4-31.4 SGGY S WS 151YIYYSGSTY 157 SYAQKFQG YNPSLKS 1-46.5 SYYM V 77 IINPSGGST 79 4-31.5SGGYYWS 147 S IYYSGSTY 158 SYAQKFQG YNPSLKS 1-46.6 SYYM S 78 IINPSGGST79 4-31.6 SGGYYWS 147 N IYYSGSTY 159 SYAQKFQG YNPSLKS 1-46.7 SYYMH 72 VINPSGGST 80 4-31.7 SGGYYWS 147 YIYYSG N TY 160 SYAQKFQG YNPSLKS 1-46.8SYYMH 72 IINP G GGST 81 4-31.8 SGGYYWS 147 YIYYSGST S 161 SYAQKFQGYNPSLKS 1-46.9 SYYMH 72 IINPSGGST 82 4-31.9 SGGYYWS 147 YIYYSGST V 162 TYAQKFQG YNPSLKS 1-69.0 SYAIS 83 GIIPIFGTA 84 4-34.0 GYYWS 163 EIDHSGSTN166 NYAQKFQG YNPSLKS 1-69.1 N YAIS 41 GIIPIFGTA 84 4-34.1 D YYWS 164EIDHSGSTN 166 NYAQKFQG YNPSLKS 1-69.2  S L AIS 42 GIIPIFGTA 84 4-34.2GYYW T 165 EIDHSGSTN 166 NYAQKFQG YNPSLKS 1-69.3  SY G IS 43 GIIPIFGTA84 4-34.3 GYYWS 163 D IDHSGSTN 167 NYAQKFQG YNPSLKS 1-69.4  SY T IS 44GIIPIFGTA 84 4-34.4 GYYWS 163 EI S HSGSTN 168 NYAQKFQG YNPSLKS 1-69.5 SYAI N 45 GIIPIFGTA 84 4-34.5 GYYWS 163 EID Q SGSTN 169 NYAQKFQG YNPSLKS1-69.6  SYAIS 83 S IIPIFGTA 46 4-34.6 GYYWS 163 EIDH G GSTN 170 NYAQKFQGYNPSLKS 1-69.7  SYAIS 83 GI A PIFGTA 47 4-34.7 GYYWS 163 EIDHSG N TN 171NYAQKFQG YNPSLKS 1-69.8  SYAIS 83 GIIPI L GTA 48 4-34.8 GYYWS 163EIDHSGST S 172 NYAQKFQG YNPSLKS 1-69.9  SYAIS 83 GIIPIFGTA 49 4-34.9GYYWS 163 EIDHSGST D 173 S YAQKFQG YNPSLKS 3-15.0  NAWMS 85 RIKSKTDGG 914-39.0 SSSYYWG 174 SIYYSGSTY 181 TTDYAAPVKG YNPSLKS 3-15.1  K AWMS 86RIKSKTDGG 91 4-39.1 T SSYYWG 175 SIYYSGSTY 181 TTDYAAPVKG YNPSLKS3-15.2  D AWMS 87 RIKSKTDGG 91 4-39.2 S N SYYWG 176 SIYYSGSTY 181TTDYAAPVKG YNPSLKS 3-15.3 NA L MS 88 RIKSKTDGG 91 4-39.3 SS D YYWG 177SIYYSGSTY 181 TTDYAAPVKG YNPSLKS 3-15.4 NA A MS 89 RIKSKTDGG 91 4-39.4SS N YYWG 178 SIYYSGSTY 181 TTDYAAPVKG YNPSLKS 3-15.5 NAWM N 90RIKSKTDGG 91 4-39.5 SS R YYWG 179 SIYYSGSTY 181 TTDYAAPVKG YNPSLKS3-15.6 NAWMS 85 S IKSKTDGG 92 4-39.6 SSSY A WG 180 SIYYSGSTY 181TTDYAAPVKG YNPSLKS 3-15.7 NAWMS 85 RIKS T TDGG 93 4-39.7 SSSYYWG 174 NIYYSGSTY 182 TTDYAAPVKG YNPSLKS 3-15.8 NAWMS 85 RIKSK A DGG 94 4-39.8SSSYYWG 174 SI S YSGSTY 183 TTDYAAPVKG YNPSLKS 3-15.9 NAWMS 85 RIKSKTDGG95 4-39.9 SSSYYWG 174 SIYYSGST S 184 TT G YAAPVKG YNPSLKS 3-23.0 SYAMS96 AISGSGGST 100 4-59.0 SYYWS 185 YIYYSGST N 189 YYADSVKG YNPSLKS 3-23.1N YAMS 97 AISGSGGST 100 4-59.1 T YYWS 186 YIYYSGSTN 189 YYADSVKG YNPSLKS3-23.2 T YAMS 98 AISGSGGST 100 4-59.2 S S YWS 187 YIYYSGSTN 189 YYADSVKGYNPSLKS 3-23.3 S S AMS 99 AISGSGGST 100 4-59.3 SY S WS 188 YIYYSGSTN 189YYADSVKG YNPSLKS 3-23.4 SYAMS 96 G ISGSGGST 101 4-59.4 SYYWS 185 FIYYSGSTN 190 YYADSVKG YNPSLKS 3-23.5 SYAMS 96 S ISGSGGST 102 4-59.5SYYWS 185 H IYYSGSTN 191 YYADSVKG YNPSLKS 3-23.6 SYAMS 96 T ISGSGGST 1034-59.6 SYYWS 185 S IYYSGSTN 192 YYADSVKG YNPSLKS 3-23.7 SYAMS 96 VISGSGGST 104 4-59.7 SYYWS 185 YIY S SGSTN 193 YYADSVKG YNPSLKS 3-23.8SYAMS 96 AIS A SGGST 105 4-59.8 SYYWS 185 YIYYSGST D 194 YYADSVKGYNPSLKS 3-23.9 SYAMS 96 AISGSGGST 106 4-59.9 SYYWS 185 YIYYSGST T 195 SYADSVKG YNPSLKS 3-30.0 SYGMH 107 VISYDGSNK 111 4-61.0 SGSYYWS 196YIYYSGSTN 202 YYADSVKG YNPSLKS 3-30.1 NYGMH 108 VISYDGSNK 111 4-61.1 SGG YYWS 197 YIYYSGSTN 202 YYADSVKG YNPSLKS 3-30.2 SY A MH 109 VISYDGSNK111 4-61.2 SG N YYWS 198 YIYYSGSTN 202 YYADSVKG YNPSLKS 3-30.3 SYG F H110 VISYDGSNK 111 4-61.3 SGS S YWS 199 YIYYSGSTN 202 YYADSVKG YNPSLKS3-30.4 SYGMH 107 F ISYDGSNK 112 4-61.4 SGSY S WS 200 YIYYSGSTN 202YYADSVKG YNPSLKS 3-30.5 SYGMH 107 L ISYDGSNK 113 4-61.5 SGSYYW T 201YIYYSGSTN 202 YYADSVKG YNPSLKS 3-30.6 SYGMH 107 VIS S DGSNK 114 4-61.6SGSYYWS 196 R IYYSGSTN 203 YYADSVKG YNPSLKS 3-30.7 SYGMH 107 VISYDG N NK115 4-61.7 SGSYYWS 196 S IYYSGSTN 204 YYADSVKG YNPSLKS 3-30.8 SYGMH 107VISYDGS I K 116 4-61.8 SGSYYWS 196 YIY T SGSTN 205 YYADSVKG YNPSLKS3-30.9 SYGMH 107 VISYDGSN Q 117 4-61.9 SGSYYWS 196 YIYYSGST S 206YYADSVKG YNPSLKS 3-33.0 SYGMH 118 VIWYDGSNK 124 4-B.0  SGYYWG 207SIYHSGSTY 212 YYADSVKG YNPSLKS 3-33.1 T YGMH 119 VIWYDGSNK 124 4-B.1  SA YYWG 208 SIYHSGSTY 212 YYADSVKG YNPSLKS 3-33.2 N YGMH 120 VIWYDGSNK124 4-B.2  SG S YWG 209 SIYHSGSTY 212 YYADSVKG YNPSLKS 3-33.3 S S GMH121 VIWYDGSNK 124 4-B.3  SGY N WG 210 SIYHSGSTY 212 YYADSVKG YNPSLKS3-33.4 SY A MH 122 VIWYDGSNK 124 4-B.4  SGYYW A 211 SIYHSGSTY 212YYADSVKG YNPSLKS 3-33.5 SYGM N 123 VIWYDGSNK 124 4-B.5  SGYYWG 207 TIYHSGSTY 213 YYADSVKG YNPSLKS 3-33.6 SYGMH 118 L IWYDGSNK 125 4-B.6 SGYYWG 207 S S YHSGSTY 214 YYADSVKG YNPSLKS 3-33.7 SYGMH 118 F IWYDGSNK126 4-B.7  SGYYWG 207 SIYHSG N TY 215 YYADSVKG YNPSLKS 3-33.8 SYGMH 118VIWYDGSNK 127 4-B.8  SGYYWG 207 SIYHSGST N 216 S YADSVKG YNPSLKS 3-33.9SYGMH 118 VIWYDGSNK 128 4-B.9  SGYYWG 207 SIYHSGST G 217 G YADSVKGYNPSLKS 5-51.0 SYWIG 218 IIYPGDSDT 224 RYSPSFQG 5-51.1 T YWIG 219IIYPGDSDT 224 RYSPSFQG 5-51.2 N YWIG 220 IIYPGDSDT 224 RYSPSFQG 5-51.3 SN WIG 221 IIYPGDSDT 224 RYSPSFQG 5-51.4 SY Y IG 222 IIYPGDSDT 224RYSPSFQG 5-51.5 SYWI S 223 IIYPGDSDT 224 RYSPSFQG 5-51.6 SYWIG 218 SIYPGDSDT 225 RYSPSFQG 5-51.7 SYWIG 218 IIYP A DSDT 226 RYSPSFQG 5-51.8SYWIG 218 IIYPGDS S T 227 RYSPSFQG 5-51.9 SYWIG 218 IIYPGDSDT 228 TYSPSFQG ¹Contains an N-linked glycosylation site which can be removed,if desired, as described herein.

As specified in the Detailed Description, other criteria can be used toselect which amino acids are to be altered and the identity of theresulting altered sequence. This is true for any heavy chain chassissequence, or any other sequence of the invention. The approach outlinedabove is meant for illustrative purposes and is non-limiting.

Example 3 Design of an Exemplary VK Chassis Library

This example describes the design of an exemplary VK chassis library.One of ordinary skill in the art will recognize that similar principlesmay be used to design a Vλ library, or a library containing both VK andVλ chassis. Design of a Vλ chassis library is presented in Example 4.

As was previously demonstrated in Example 1, for IGHV germlinesequences, the sequence characteristics and occurrence of human IGKVgermline sequences in antibodies from peripheral blood were analyzed.The data are presented in Table 9.

TABLE 9 IGKV Gene Characteristics and Occurrence in Antibodies fromPeripheral Blood Estimated Relative Alternative CDRL1 CDRL2 CanonicalOccurrence in IGKV Gene Names Length Length Structures¹ PeripheralBlood² IGKV1-05 L12 11 7 2-1-(U) 69  IGKV1-06 L11 11 7 2-1-(1) 14 IGKV1-08 L9 11 7 2-1-(1) 9 IGKV1-09 L8 11 7 2-1-(1) 24  IGKV1-12 L5, L1911 7 2-1-(1) 32  IGKV1-13 L4, L18 11 7 2-1-(1) 13  IGKV1-16 L1 11 72-1-(1) 15  IGKV1-17 A30 11 7 2-1-(1) 34  IGKV1-27 A20 11 7 2-1-(1) 27 IGKV1-33 O8, O18 11 7 2-1-(1) 43  IGKV1-37 O14, O4 11 7 2-1-(1) 3IGKV1-39 O2, O12 11 7 2-1-(1) 147  IGKV1D-16 L15 11 7 2-1-(1) 6IGKV1D-17 L14 11 7 2-1-(1) 1 IGKV1D-43 L23 11 7 2-1-(1) 1 IGKV1D-8 L2411 7 2-1-(1) 1 IGKV2-24 A23 16 7 4-1-(1) 8 IGKV2-28 A19, A3 16 7 4-1-(1)62  IGKV2-29 A18 16 7 4-1-(1) 6 IGKV2-30 A17 16 7 4-1-(1) 30  IGKV2-40O1, O11 17 7 3-1-(1) 3 IGKV2D-26 A8 16 7 4-1-(1) 0 IGKV2D-29 A2 16 74-1-(1) 20  IGKV2D-30 A1 16 7 4-1-(1) 4 IGKV3-11 L6 11 7 2-1-(1) 87 IGKV3-15 L2 11 7 2-1-(1) 53  IGKV3-20 A27 12 7 6-1-(1) 195  IGKV3D-07L25 12 7 6-1-(1) 0 IGKV3D-11 L20 11 7 2-1-(U) 0 IGKV3D-20 A11 12 76-1-(1) 2 IGKV4-1 B3 17 7 3-1-(1) 83  IGKV5-2 B2 11 7 2-1-(1) 1 IGKV6-21A10, A26 11 7 2-1-(1) 6 IGKV6D-41 A14 11 7 2-1-(1) 0 ¹Adapted fromTomlinson et al. EMBO J., 1995, 14: 4628, incorporated by reference inits entirety. The number in parenthesis refers to canonical structuresin CDRL3, if one assuming the most common length (see Example 5 forfurther detail about CDRL3). ²Estimated from sets of human VK sequencescompiled from the NCBI database; full set of GI numbers provided inAppendix A.

The 14 most commonly occurring IGKV germline genes (bolded in column 6of Table 9) account for just over 90% of the usage of the entirerepertoire in peripheral blood. From the analysis of Table 9, ten IGKVgermline genes were selected for representation as chassis in thecurrently exemplified library (Table 10). All but V1-12 and V1-27 areamong the top 10 most commonly occurring. IGKV germline genes VH2-30,which was tenth in terms of occurrence in peripheral blood, was notincluded in the currently exemplified embodiment of the library, inorder to maintain the proportion of chassis with short (i.e., 11 or 12residues in length) CDRL1 sequences at about 80% in the final set of 10chassis. V1-12 was included in its place. V1-17 was more similar toother members of the V1 family that were already selected; therefore,V1-27 was included, instead of V1-17. In other embodiments, the librarycould include 12 chassis (e.g., the ten of Table 10 plus V1-17 andV2-30), or a different set of any “N” chassis, chosen strictly byoccurrence (Table 9) or any other criteria. The ten chosen VK chassisaccount for about 80% of the usage in the data set believed to berepresentative of the entire kappa light chain repertoire.

TABLE 10 VK Chassis Selected for Use in the Exemplary Library EstimatedRelative CDR-L1 CDR-L2 Canonical Occurrence in Chassis Length LengthStructures Peripheral Blood VK1-5 11 7 2-1-(U) 69 VK1-12 11 7 2-1-(1) 32VK1-27 11 7 2-1-(1) 27 VK1-33 11 7 2-1-(1) 43 VK1-39 11 7 2-1-(1) 147VK2-28 16 7 4-1-(1) 62 VK3-11 11 7 2-1-(1) 87 VK3-15 11 7 2-1-(1) 53VK3-20 12 7 6-1-(1) 195 VK4-1 17 7 3-1-(1) 83

The amino acid sequences of the selected VK chassis enumerated in Table10 are provided in Table 11.

TABLE 11 Amino Acid Sequences for VK Chassis Selected for Inclusion in the Exemplary Library SEQ Chassis FRM1 CDRL1 FRM2 CDRL2FRM3 CDRL3¹ ID NO: VK1-5 DIQMTQS RASQSI WYQQKP DASSLE GVPSRFSGSGSGTQQYNS 229 PSTLSAS SSWLA GKAPKL S EFTLTISSLQPDD YS VGDRVTI LIY FATYYC TCVK1-12 DIQMTQS RASQGI WYQQKP AASSLQ GVPSRFSGSGSGT QQANS 230 PSSVSASSSWLA GKAPKL S DFTLTISSLQPED FP VGDRVTI LIY FATYYC TC VK1-27 DIQMTQSRASQGI WYQQKP AASTLQ GVPSRFSGSGSGT QKYNS 231 PSSLSAS SNYLA GKVPKL SDFTLTISSLQPED AP VGDRVTI LIY VATYYC TC VK1-33 DIQMTQS QASQDI WYQQKPDASNLE GVPSRFSGSGSGT QQYDN 232 PSSLSAS SNYLN GKAPKL T DFTFTISSLQPED LPVGDRVTI LIY IATYYC TC VK1-39 DIQMTQS RASQSI WYQQKP AASSLQ GVPSRFSGSGSGTQQSYS 233 PSSLSAS SSYLN GKAPKL S DFTLTISSLQPED TP VGDRVTI LIY FATYYC TCVK2-28 DIVMTQS RSSQSL WYLQKP LGSNRA GVPDRFSGSGSGT MQALQ 234 PLSLPVTLHSNGY GQSPQL S DFTLKISRVEAED TP PGEPASI NYLD LIY VGVYYC SC VK3-11EIVLTQS RASQSV WYQQKP DASNRA GIPARFSGSGSGT QQRSN 235 PATLSLS SSYLAGQAPRL T DFTLTISSLEPED WP PGERATL LIY FAVYYC SC VK3-15 EIVMTQS RASQSVWYQQKP GASTRA GIPARFSGSGSGT QQYNN 236 PATLSVS SSNLA GQAPRL TEFTLTISSLQSED WP PGERATL LIY FAVYYC SC VK3-20 EIVLTQS RASQSV WYQQKPGASSRA GIPDRFSGSGSGT QQYGS 237 PGTLSLS SSSYLA GQAPRL T DFTLTISRLEPED SPPGERATL LIY FAVYYC SC VK4-1 DIVMTQS KSSQSV WYQQKP WASTRE GVPDRFSGSGSGTQQYYS 238 PDSLAVS LYSSNN GQPPKL S DFTLTISSLQAED TP LGERATI KNYLA LIYVAVYYC NC ¹Note that the portion of the IGKV gene contributing to VKCDR3is not considered part of the chassis as described herein. The VKchassis is defined as Kabat residues 1 to 88 of the IGKV-encodedsequence, or from the start of FRM1 to the end of FRM3. The portion ofthe VKCDR3 sequence contributed by the IGKV gene is referred to hereinas the L3-VK region.

Example 4 Design of an Exemplary Vλ Chassis Library

This example, describes the design of an exemplary Vλ chassis library.As was previously demonstrated in Examples 1-3, for the VH and VKchassis sequences, the sequence characteristics and occurrence of humanIgλN germline-derived sequences in peripheral blood were analyzed. Aswith the assignment of other sequences set forth herein to germlinefamilies, assignment of Vλ sequences to a germline family was performedvia SoDA and VBASE2 (Volpe and Kepler, Bioinformatics, 2006, 22: 438;Mollova et al., BMS Systems Biology, 2007, IS: P30, each incorporated byreference in its entirety). The data are presented in Table 12.

TABLE 12 IGλV Gene Characteristics and Occurrence in Peripheral BloodContribution of Estimated Relative IGλV Alternative Canonical IGVλ Geneto Occurrence in Gene Name Structures¹ CDRL3 Peripheral Blood² IGλV3-13R 11-7(*) 8 11.5 IGλV3-21 3H 11-7(*) 9 10.5 IGλV2-14 2A2 14-7(A) 9 10.1IGλV1-40 1E 14-7(A) 9 7.7 IGλV3-19 3L 11-7(*) 9 7.6 IGλV1-51 1B 13-7(A)9 7.4 IGλV1-44 1C 13-7(A) 9 7.0 IGλV6-57 6A 13-7(B) 7 6.1 IGλV2-8 2C14-7(A) 9 4.7 IGλV3-25 3M 11-7(*) 9 4.6 IGλV2-23 2B2 14-7(A) 9 4.3IGλV3-10 3P 11-7(*) 9 3.4 IGλV4-69 4B 12-11(*) 7 3.0 IGλV1-47 1G 13-7(A)9 2.9 IGλV2-11 2E 14-7(A) 9 1.3 IGλV7-43 7A 14-7(B) 8 1.3 IGλV7-46 7B14-7(B) 8 1.1 IGλV5-45 5C 14-11(*) 8 1.0 IGλV4-60 4A 12-11(*) 7 0.7IGλV10-54 8A 14-7(B) 8 0.7 IGλV8-61 10A 13-7(C) 9 0.7 IGλV3-9 3J 11-7(*)8 0.6 IGλV1-36 1A 13-7(A) 9 0.4 IGλV2-18 2D 14-7(A) 9 0.3 IGλV3-16 3A11-7(*) 9 0.2 IGλV3-27 11-7(*) 7 0.2 IGλV4-3 5A 14-11(*) 8 0.2 IGλV5-394C 12-11(*) 12 0.2 IGλV9-49 9A 12-12(*) 12 0.2 IGλV3-12 3I 11-7(*) 9 0.1¹Adapted from Williams et al. J. Mol. Biol. 1996: 264, 220-32. The (*)indicates that the canonical structure is entirely defined by thelengths of CDRs L1 and L2. When distinct structures are possible foridentical L1 and L2 length combinations, the structure present in agiven gene is set forth as A, B, or C. ²Estimated from a set of human Vλsequences compiled from the NCBI database; full set of GI codes setforth in Appendix B.

To choose a subset of the sequences from Table 12 to serve as chassis,those represented at less than 1% in peripheral blood (as extrapolatedfrom analysis of published sequences corresponding to the GI codesprovided in Appendix B) were first discarded. From the remaining 18germline sequences, the top occurring genes for each unique canonicalstructure and contribution to CDRL3, as well as any germline generepresented at more than the 5% level, were chosen to constitute theexemplary Vλ chassis. The list of 11 such sequences is given in Table13, below. These 11 sequences represent approximately 73% of therepertoire in the examined data set (Appendix B).

TABLE 13 Vλ Chassis Selected for Use in the Exemplary Library CDRL1CDRL2 Canonical Relative Chassis Length Length Structure OccurrenceVλ3-1 11 7 11-7(*) 11.5 Vλ3-21 11 7 11-7(*) 10.5 Vλ2-14 14 7 14-7(A)10.1 Vλ1-40 14 7 14-7(A) 7.7 Vλ3-19 11 7 11-7(*) 7.6 Vλ1-51 13 7 13-7(A)7.4 Vλ1-44 13 7 13-7(A) 7.0 Vλ6-57 13 7 13-7(B) 6.1 Vλ4-69 12 1112-11(*) 3.0 Vλ7-43 14 7 14-7(B) 1.3 Vλ5-45 11 11 14-11(*) 1.0

The amino acid sequences of the selected Vλ chassis enumerated in Table13 are provided in Table 14, below.

TABLE 14 Amino Acid Sequences for Vλ Chassis Selectedfor Inclusion in the Exemplary Library Chassis FRM1 CDRL1 FRM2 CDRL2FRM3 CDRL3² Vλ1-40  QSVLTQP TGSSSN WYQQLP  GN---- GVPDRFSGSKSG-- QSYDSSSEQ ID PSVSGAP IGAGYD GTAPKL  SNRPS TSASLAITGLQAEDE  LSG NO: 531 GQRVTIS ---VH LIY ADYYC C Vλ1-44  QSVLTQP SGSSSN WYQQLP  SN----GVPDRFSGSKSG-- AAWDDS SEQ ID PSASGTP IGSNT- GTAPKL  NQRPSTSASLAISGLQSEDE  LNG NO: 532  GQRVTIS ---VN LIY ADYYC C Vλ1-51  QSVLTQPSGSSSN WYQQLP  DN---- GIPDRFSGSKSG-- GTWDSS SEQ ID PSVSAAP IGNNY-GTAPKL  NKRPS TSATLGITGLQTGDE  LSA NO: 533  GQKVTIS ---VS LIY ADYYC CVλ2-14 QSALTQP TGTSSD WYQQHP  EV---- GVSNRFSGSKSG-- SSYTSS SEQ IDASVSGSP VGGYNY GKAPKL  SNRPS NTASLTISGLQAEDE  STL NO: 534  GQSITIS ---VSMIY ADYYC C Vλ3-1¹  SYELTQP SGDKLG WYQQKP  QD---- GIPERFSGSNSG-- QAWDSSSEQ ID PSVSVSP DKY--- GQSPVL  SKRPS NTATLTISGTQAMDE  TA- NO: 535 GQTASIT ---A S VIY ADYYC C Vλ3-19  SSELTQD QGDSLR WYQQKP  GK----GIPDRFSGSSSG-- NSRDSS SEQ ID PAVSVAL SYY--- GQAPVL  NNRPSNTASLTITGAQAEDE  GNH NO: 536  GQTVRIT ---AS VIY ADYYC C Vλ3-21 SYVLTQPGGNNIG WYQQKP  YD---- GIPERFSGSNSG-- QVWDSS SEQ ID PSVSVAP SKS---GQAPVL  SDRPS NTATLTISRVEAGDE  SDH NO: 537  GKTARIT ---VH VIY ADYYC CVλ4-69 QLVLTQS TLSSGH WHQQQP  LNSDGS GIPDRFSGSSSG-- QTWGTG SEQ IDPSASASL SSYA-- EKGPRY  HSKGD AERYLTISSLQSEDE  I-- NO: 538  GASVKLT ---IALMK ADYYC C Vλ6-57 NFMLTQP TRSSGS WYQQRP  ED---- GVPDRFSGSIDSSSN  QSYDSSSEQ ID HSVSESP IASNY- GSSPTT  NQRPS SASLTISGLKTEDEA  N-- NO: 539 GKTVTIS ---VQ VIY DYYC C Vλ5-45 QAVLTQP TLRSGI WYQQKP  YKSDSDGVPSRFSGSKDASAN  MIWHSS SEQ ID ASLSASP NVGTYR GSPPQY  KQQGSAGILLISGLQSEDEA  AS- NO: 540  GASASLT ---IY LLR DYYC C Vλ7-43 QTVVTQEASSTGA WFQQKP  ST---- WTPARFSGSLLG-- LLYYGG SEQ ID PSLTVSP VTSGYYGQAPRA  SNKHS GKAALTLSGVQPEDE  AQ- NO: 541  GGTVTLT ---PN LIY AEYYC C¹The last amino acid in CDRL1 of the Vλ3-1 chassis, S, differs from thecorresponding one in the IGλV3-1 germline gene, C. This was done toavoid having a potentially unpaired CYS (C) amino acid in the resultingsynthetic light chain. ²Note that, as for the VK chassis, the portion ofthe IGλV gene contributing to VλCDR3 is not considered part of thechassis as described herein. The Vλ chassis is defined as Kabat residues1 to 88 of the IGλV-encoded sequence, or from the start of FRM1 to theend of FRM3. The portion of the VλCDR3 sequence contributed by the IGλVgene is referred to herein as the L3-Vλ region.

Example 5 Design of a CDRH3 Library

This example describes the design of a CDHR3 library from its individualcomponents. In nature, the CDRH3 sequence is derived from a complexprocess involving recombination of three different genes, termed IGHV,IGHD and IGHJ. In addition to recombination, these genes may alsoundergo progressive nucleotide deletions: from the 3′ end of the IGHVgene, either end of the IGHD gene, and/or the 5′ end of the IGHJ gene.Non-templated nucleotide additions may also occur at the junctionsbetween the V, D and J sequences. Non-templated additions at the V-Djunction are referred to as “N1”, and those at the D-J junction arereferred to as “N2”. The D gene segments may be read in three forwardand, in some cases, three reverse reading frames.

In the design of the present exemplary library, the codon (nucleotidetriplet) or single amino acid was designated as a fundamental unit, tomaintain all sequences in the desired reading frame. Thus, all deletionsor additions to the gene segments are carried out via the addition ordeletion of amino acids or codons, and not single nucleotides. Accordingto the CDRH3 numbering system of this application, CDRH3 extends fromamino acid number 95 (when present; see Example 1) to amino acid 102.

Example 5.1 Selection of the DH Segments

In this illustrative example, selection of DH gene segments for use inthe library was performed according to principles similar to those usedfor the selection of the chassis sequences. First, an analysis of IGHDgene usage was performed, using data from Lee et al., Immunogenetics,2006, 57: 917; Corbett et al., PNAS, 1982, 79: 4118; and Souto-Carneiroet al., J. Immunol., 2004, 172: 6790 (each incorporated by reference inits entirety), with preference for representation in the library givento those IGHD genes most frequently observed in human sequences. Second,the degree of deletion on either end of the IGHD gene segments wasestimated by comparison with known heavy chain sequences, using the SoDAalgorithm (Volpe et al., Bioinformatics, 2006, 22: 438, incorporated byreference in its entirety) and sequence alignments. For the presentlyexemplified library, progressively deleted DH segments, as short asthree amino acids, were included. As enumerated in the DetailedDescription, other embodiments of the invention comprise DH segmentswith deletions to a different length, for example, about 1, 2, 4, 5, 6,7, 8, 9, or 10 amino acids. Table 15 shows the relative occurrence ofIGHD gene usage in human antibody heavy chain sequences isolated mainlyfrom peripheral blood B cells (list adapted from Lee et al.,Immunogenetics, 2006, 57: 917, incorporated by reference in itsentirety).

TABLE 15 Usage of IGHD Genes Based on Relative Occurrence in PeripheralBlood* Estimated Relative Occurrence IGHD Gene in Peripheral Blood³IGHD3-10 117 IGHD3-22 111 IGHD6-19 95 IGHD6-13 93 IGHD3-3 82 IGHD2-2 63IGHD4-17 61 IGHD1-26 51 IGHD5-5/5-18¹ 49 IGHD2-15 47 IGHD6-6 38 IGHD3-932 IGHD5-12 29 IGHD5-24 29 IGHD2-21 28 IGHD3-16 18 IGHD4-23 13 IGHD1-1 9IGHD1-7 9 IGHD4-4/4-11² 7 IGHD1-20 6 IGHD7-27 6 IGHD2-8 4 IGHD6-25 3¹Although distinct genes in the genome, the nucleotide sequences ofIGHD5-5 and IGHD5-18 are 100% identical and thus indistinguishable inrearranged VH sequences. ²IGHD4-4 and IGHD4-11 are also 100% identical.³Adapted from Lee et al. Immunogenetics, 2006, 57: 917, by merging theinformation for distinct alleles of the same IGHD gene. *IGHD1-14 mayalso be included in the libraries of the invention.

The translations of the ten most commonly expressed IGHD gene sequencesfound in naturally occurring human antibodies, in three reading frames,are shown in Table 16. Those reading frames which occur most commonly inperipheral blood have been highlighted in gray. As in Table 15, dataregarding IGHD sequence usage and reading frame statistics were derivedfrom Lee et al., 2006, and data regarding IGHD sequence reading frameusage were further complemented by data derived from Corbett et al.,PNAS, 1982, 79: 4118 and Souto-Carneiro et al., J. Immunol, 2004, 172:6790, each of which is incorporated by reference in its entirety.

TABLE 16 Translations of the Ten Most Common Naturally Occurring IGHDSequences, in Three Reading Frames (RF)

#represents a stop codon. Reading frames highlighted in gray correspondto the most commonly used reading frames.

In the presently exemplified library, the top 10 IGHD genes mostfrequently used in heavy chain sequences occurring in peripheral bloodwere chosen for representation in the library. Other embodiments of thelibrary could readily utilize more or fewer D genes. The amino acidsequences of the selected IGHD genes, including the most commonly usedreading frames and the total number of variants after progressive N- andC-terminal deletion to a minimum of three residues, are listed in Table17. As depicted in Table 17, only the most commonly occurring alleles ofcertain IGHD genes were included in the illustrative library. This is,however, not required, and other embodiments of the invention mayutilize IGHD reading frames that occur less frequently in the peripheralblood.

TABLE 17 D Genes Selected for use  in the Exemplary Library IGHD Amino Acid SEQ Total Number Gene¹ Sequence ID NO: of Variants²IGHD1-26_1 GIVGATT 13 15 IGHD1-26_3 YSGSYY 14 10 IGHD2-2_2 GYCSSTSCYT 10  9³ IGHD2-2_3 DIVVVPAAM 11 28 IGHD2-15_2 GYCSGGSCYS 16  9 IGHD3-3_3ITIFGVVII 9 28 IGHD3-10_1 VLLWFGELL 1 28 IGHD3-10_2 YYYGSGSYYN 2 36IGHD3-10_3 ITMVRGVII 3 28 IGHD3-22_2 YYYDSSGYYY 4 36 IGHD4-17_2 DYGDY 12 6 IGHD5-5_3 GYSYGY 15 10 IGHD6-13_1 GYSSSWY 7 15 IGHD6-13_2 GIAAAG 8 10IGHD6-19_1 GYSSGWY 5 15 IGHD6-19_2 GIAVAG 6 10 ¹The reading frame (RF)is specified as _RF after the name of the gene. ²In most cases the totalnumber of variants is given by (N-1) times (N-2) divided by two, where Nis the total length in amino acids of the intact D segment. ³As detailedherein, the number of variants for segments containing a putativedisulfide bond (two C or Cys residues) is limited in this illustrativeembodiment.

For each of the selected sequences of Table 17, variants were generatedby systematic deletion from the N- and/or C-termini, until there werethree amino acids remaining. For example, for the IGHD4-17_(—)2 above,the full sequence DYGDY (SEQ ID NO: 12) may be used to generate theprogressive deletion variants: DYGD (SEQ ID NO: 613), YGDY (SEQ ID NO:614), DYG, GDY and YGD. In general, for any full-length sequence of sizeN, there will be a total of (N-1)*(N-2)/2 total variants, including theoriginal full sequence. For the disulfide-loop-encoding segments, asexemplified by reading frame 2 of both IGHD2-2 and IGHD2-15, (i.e.,IGHD2-2_(—)2 and IGH2-15_(—)2), the progressive deletions were limited,so as to leave the loop intact i.e., only amino acids N-terminal to thefirst Cys, or C-terminal to the second Cys, were deleted in therespective DH segment variants. The foregoing strategy was used to avoidthe presence of unpaired cysteine residues in the exemplified version ofthe library. However, as discussed in the Detailed Description, otherembodiments of the library may include unpaired cysteine residues, orthe substitution of these cysteine residues with other amino acids. Inthe cases where the truncation of the IGHD gene is limited by thepresence of the Cys residues, only 9 variants (including the originalfull sequence) were generated; e.g., for IGHD2-22, the variants wouldbe: GYCSSTSCYT (SEQ ID NO: 10), GYCSSTSCY (SEQ ID NO: 615), YCSSTSCYT(SEQ ID NO: 616), CSSTSCYT (SEQ ID NO: 617), GYCSSTSC (SEQ ID NO: 618),YCSSTSCY (SEQ ID NO: 619), CSSTSCY (SEQ ID NO: 620), YCSSTSC (SEQ ID NO:621) and CSSTSC (SEQ ID NO: 622).

According to the criteria outlined above, 293 DH sequences were obtainedfrom the selected IGHD gene segments, including the original IGHD genesegments. Certain sequences are redundant. For example, it is possibleto obtain the YYY variant from either IGHD3-10_(—)2 (full sequenceYYYGSGSYYN (SEQ ID NO: 2)), or in two different ways from IGHD3-22_(—)2(SEQ ID NO: 4) (YYYDSSGYYY). When redundant sequences are removed, thenumber of unique DH segment sequences in this illustrative embodiment ofthe library is 278. These sequences are enumerated in Table 18.

TABLE 18 DH Gene Segments Used in the  Presently Exemplified Library*DH Segment SEQ DH Segment SEQ ID Designation¹ Peptide ID NO: DesignationPeptide NO: IGHD1-26_1-1 ATT IGHD3-10_2-20 YYGSG 713 IGHD1-26_1-2 GATIGHD3-10_2-21 YYYGS 714 IGHD1-26_1-3 GIV IGHD3-10_2-22 GSGSYY 715IGHD1-26_1-4 IVG IGHD3-10_2-23 SGSYYN 716 IGHD1-26_1-5 VGA IGHD3-10_2-24YGSGSY 717 IGHD1-26_1-6 GATT 623 IGHD3-10_2-25 YYGSGS 718 IGHD1-26_1-7GIVG 624 IGHD3-10_2-26 YYYGSG 719 IGHD1-26_1-8 IVGA 625 IGHD3-10_2-27GSGSYYN 720 IGHD1-26_1-9 VGAT 626 IGHD3-10_2-28 YGSGSYY 721IGHD1-26_1-10  GIVGA 627 IGHD3-10_2-29 YYGSGSY 722 IGHD1-26_1-11  IVGAT628 IGHD3-10_2-30 YYYGSGS 723 IGHD1-26_1-12  VGATT 629 IGHD3-10_2-31YGSGSYYN 724 IGHD1-26_1-13  GIVGAT 630 IGHD3-10_2-32 YYGSGSYY 725IGHD1-26_1-14  IVGATT 631 IGHD3-10_2-33 YYYGSGSY 726 IGHD1-26_1-15GIVGATT 13 IGHD3-10_2-34 YYGSGSYYN 727 IGHD1-26_3-1 YSG IGHD3-10_2-35YYYGSGSYY 728 IGHD1-26_3-2 YSGS 632 IGHD3-10_2-36 YYYGSGSYYN 2IGHD1-26_3-3 YSGSY 633 IGHD3-10_3-1 GVI IGHD1-26_3-4 YSGSYY 14IGHD3-10_3-2 ITM IGHD2-02_2-1 CSSTSC 622 IGHD3-10_3-3 MVR IGHD2-02_2-2CSSTSCY 620 IGHD3-10_3-4 RGV IGHD2-02_2-3 YCSSTSC 621 IGHD3-10_3-5 TMVIGHD2-02_2-4  CSSTSCYT 617 IGHD3-10_3-6 VII IGHD2-02_2-5  GYCSSTSC 618IGHD3-10_3-7 VRG IGHD2-02_2-6  YCSSTSCY 619 IGHD3-10_3-8 GVII 729IGHD2-02_2-7  GYCSSTSCY 615 IGHD3-10_3-9 ITMV 730 IGHD2-02_2-8 YCSSTSCYT 616 IGHD3-10_3-10 MVRG 731 IGHD2-02_2-9 GYCSSTSCYT 10IGHD3-10_3-11 RGVI 732 IGHD2-02_3-1 AAM IGHD3-10_3-12 TMVR 733IGHD2-02_3-2 DIV IGHD3-10_3-13 VRGV 734 IGHD2-02_3-3 IVV IGHD3-10_3-14ITMVR 735 IGHD2-02_3-4 PAA IGHD3-10_3-15 MVRGV 736 IGHD2-02_3-5 VPAIGHD3-10_3-16 RGVII 737 IGHD2-02_3-6 VVP IGHD3-10_3-17 TMVRG 738IGHD2-02_3-7 VVV IGHD3-10_3-18 VRGVI 739 IGHD2-02_3-8 DIVV 634IGHD3-10_3-19 ITMVRG 740 IGHD2-02_3-9 IVVV 635 IGHD3-10_3-20 MVRGVI 741IGHD2-02_3-10 PAAM 636 IGHD3-10_3-21 TMVRGV 742 IGHD2-02_3-11 VPAA 637IGHD3-10_3-22 VRGVII 743 IGHD2-02_3-12 VVPA 638 IGHD3-10_3-23 ITMVRGV744 IGHD2-02_3-13 VVVP 639 IGHD3-10_3-24 MVRGVII 745 IGHD2-02_3-14 DIVVV640 IGHD3-10_3-25 TMVRGVI 746 IGHD2-02_3-15 IVVVP 641 IGHD3-10_3-26ITMVRGVI 747 IGHD2-02_3-16  VPAAM 642 IGHD3-10_3-27 TMVRGVII 748IGHD2-02_3-17  VVPAA 643 IGHD3-10_3-28 ITMVRGVII 3 IGHD2-02_3-18  VVVPA644 IGHD3-22_2-1 DSS IGHD2-02_3-19  DIVVVP 645 IGHD3-22_2-2 GYYIGHD2-02_3-20  IVVVPA 646 IGHD3-22_2-3 SGY IGHD2-02_3-21  VVPAAM 647IGHD3-22_2-4 SSG IGHD2-02_3-22  VVVPAA 648 IGHD3-22_2-5 YDSIGHD2-02_3-23  DIVVVPA 649 IGHD3-22_2-6 YYD IGHD2-02 3-24  IVVVPAA 650IGHD3-22_2-7 DSSG 749 IGHD2-02_3-25 VVVPAAM 651 IGHD3-22_2-8 GYYY 750IGHD2-02_3-26 DIVVVPAA 652 IGHD3-22_2-9 SGYY 751 IGHD2-02_3-27 IVVVPAAM653 IGHD3-22_2-10 SSGY 752 IGHD2-02_3-28 DIVVVPAAM 11 IGHD3-22_2-11 YDSS753 IGHD2-15_2-1 CSGGSC 654 IGHD3-22_2-12 YYDS 754 IGHD2-15_2-2 CSGGSCY655 IGHD3-22_2-13 YYYD 755 IGHD2-15_2-3 YCSGGSC 656 IGHD3-22_2-14 DSSGY756 IGHD2-15_2-4  CSGGSCYS 657 IGHD3-22_2-15 SGYYY 757 IGHD2-15_2-5 GYCSGGSC 658 IGHD3-22_2-16 SSGYY 758 IGHD2-15_2-6  YCSGGSCY 659IGHD3-22_2-17 YDSSG 759 IGHD2-15_2-7  GYCSGGSCY 660 IGHD3-22_2-18 YYDSS760 IGHD2-15_2-8  YCSGGSCYS 661 IGHD3-22_2-19 YYYDS 761 IGHD2-15_2-9GYCSGGSCYS 16 IGHD3-22_2-20 DSSGYY 762 IGHD3-03_3-1 FGV IGHD3-22_2-21SSGYYY 763 IGHD3-03_3-2 GVV IGHD3-22_2-22 YDSSGY 764 IGHD3-03_3-3 IFGIGHD3-22_2-23 YYDSSG 765 IGHD3-03_3-4 ITI IGHD3-22_2-24 YYYDSS 766IGHD3-03_3-5 TIF IGHD3-22_2-25 DSSGYYY 767 IGHD3-03_3-6 VVIIGHD3-22_2-26 YDSSGYY 768 IGHD3-03_3-7 FGVV 662 IGHD3-22_2-27 YYDSSGY769 IGHD3-03_3-8 GVVI 663 IGHD3-22_2-28 YYYDSSG 770 IGHD3-03 3-9 IFGV664 IGHD3-22_2-29 YDSSGYYY 771 IGHD3-03_3-10 ITIF 665 IGHD3-22_2-30YYDSSGYY 772 IGHD3-03_3-11 TIFG 666 IGHD3-22_2-31 YYYDSSGY 773IGHD3-03_3-12 VVII 667 IGHD3-22_2-32 YYDSSGYYY 774 IGHD3-03_3-13 FGVVI668 IGHD3-22_2-33 YYYDSSGYY 775 IGHD3-03_3-14 GVVII 669 IGHD3-22_2-34YYYDSSGYYY 4 IGHD3-03_3-15 IFGVV 670 IGHD4-17_2-1 DYG IGHD3-03_3-16ITIFG 671 IGHD4-17_2-2 GDY IGHD3-03_3-17 TIFGV 672 IGHD4-17_2-3 YGDIGHD3-03_3-18  FGVVII 673 IGHD4-17_2-4 DYGD 613 IGHD3-03_3-19  IFGVVI674 IGHD4-17_2-5 YGDY 614 IGHD3-03_3-20  ITIFGV 675 IGHD4-17_2-6  DYGDY12 IGHD3-03_3-21  TIFGVV 676 IGHD5-5_3-1 SYG IGHD3-03 3-22  IFGVVII 677IGHD5-5_3-2 YGY IGHD3-03 3-23  ITIFGVV 678 IGHD5-5_3-3 YSYIGHD3-03_3-24  TIFGVVI 679 IGHD5-5_3-4 GYSY 776 IGHD3-03_3-25  ITIFGVVI680 IGHD5-5_3-5 SYGY 777 IGHD3-03_3-26  TIFGVVII 681 IGHD5-5_3-6 YSYG778 IGHD3-03_3-27 ITIFGVVII 9 IGHD5-5_3-7 GYSYG 779 IGHD3-10_1-1 ELLIGHD5-5_3-8 YSYGY 780 IGHD3-10_1-2 FGE IGHD5-53-9 GYSYGY 15 IGHD3-10_1-3GEL IGHD6-13_1-1 SSS IGHD3-10_1-4 LLW IGHD6-13_1-2 SSW IGHD3-10_1-5 LWFIGHD6-13_1-3 SWY IGHD3-10_1-6 VLL IGHD6-13_1-4 SSSW 781 IGHD3-10_1-7 WFGIGHD6-13_1-5 SSWY 782 IGHD3-10_1-8 FGEL 682 IGHD6-13_1-6 YSSS 783IGHD3-10_1-9 GELL 683 IGHD6-13_1-7 GYSSS 784 IGHD3-10_1-10 LLWF 684IGHD6-13_1-8 SSSWY 785 IGHD3-10_1-11 LWFG 685 IGHD6-13_1-9 YSSSW 786IGHD3-10_1-12 VLLW 686 IGHD6-13_1-10 GYSSSW 787 IGHD3-10_1-13 WFGE 687IGHD6-13_1-11 YSSSWY 788 IGHD3-10_1-14 FGELL 688 IGHD6-13_1-12 GYSSSWY 7IGHD3-10_1-15 LLWFG 689 IGHD6-19_1-1 GWY IGHD3-10_1-16 LWFGE 690IGHD6-19_1-2 GYS IGHD3-10_1-17 VLLWF 691 IGHD6-19_1-3 SGW IGHD3-10_1-18WFGEL 692 IGHD6-19_1-4 YSS IGHD3-10_1-19 LLWFGE 693 IGHD6-19_1-5 GYSS789 IGHD3-10_1-20 LWFGEL 694 IGHD6-19_1-6 SGWY 790 IGHD3-10_1-21  VLLWFG695 IGHD6-19_1-7 SSGW 791 IGHD3-10_1-22 WFGELL 696 IGHD6-19_1-8 YSSG 792IGHD3-10_1-23  LLWFGEL 697 IGHD6-19_1-9 GYSSG 793 IGHD3-10_1-24  LWFGELL698 IGHD6-19_1-10 SSGWY 794 IGHD3-10_1-25  VLLWFGE 699 IGHD6-19_1-11YSSGW 795 IGHD3-10_1-26  LLWFGELL 700 IGHD6-19_1-12 GYSSGW 796IGHD3-10_1-27  VLLWFGEL 701 IGHD6-19_1-13 YSSGWY 797 IGHD3-10_1-28VLLWFGELL 1 IGHD6-19_1-14 GYSSGWY 5 IGHD3-10_2-1 GSG IGHD6-19_2-1 AVAIGHD3-10_2-2 GSY IGHD6-19_2-2 GIA IGHD3-10_2-3 SGS IGHD6-19_2-3 IAVIGHD3-10_2-4 SYY IGHD6-19_2-4 VAG IGHD3-10_2-5 YGS IGHD6-19_2-5 AVAG 798IGHD3-10_2-6 YYG IGHD6-19_2-6 GIAV 799 IGHD3-10_2-7 YYN IGHD6-19_2-7IAVA 800 IGHD3-10_2-8 YYY IGHD6-19_2-8 GIAVA 801 IGHD3-10_2-9 GSGS 702IGHD6-19_2-9 IAVAG 802 IGHD3-10_2-10 GSYY 703 IGHD6-19_2-10 GIAVAG 6IGHD3-10_2-11 SGSY 704 IGHD6-13_2-1 AAA IGHD3-10_2-12 SYYN 705IGHD6-13_2-2 AAG IGHD3-10_2-13 YGSG 706 IGHD6-13_2-3 IAA IGHD3-10_2-14YYGS 707 IGHD6-13_2-4 AAAG 803 IGHD3-10_2-15 YYYG 708 IGHD6-132-5 GIAA804 IGHD3-10_2-16 GSGSY 709 IGHD6-132-6 IAAA 805 IGHD3-10_2-17 GSYYN 710IGHD6-13_2-7 GIAAA 806 IGHD3-10_2-18 SGSYY 711 IGHD6-13_2-8 IAAAG 807IGHD3-102-19 YGSGS 712 IGHD6-132-9 GIAAAG 8 ¹The sequence designation isformatted as follows: (IGHD Gene Name)_(Reading Frame)-(Variant Number)*Note that the origin of certain variants is rendered somewhat arbitrarywhen redundant segments are deleted from the library (i.e., certainsegments may have their origins with more than one parent, including theone specified in the table).

Table 19 shows the length distribution of the 278 DH segments selectedaccording to the methods described above.

TABLE 19 Length Distributions of DH Segments Selected for Inclusion inthe Exemplary Library Number of DH Size Occurrences 3 78 4 64 5 50 6 387 27 8 20 9 12 10 4

As specified above, based on the CDRH3 numbering system defined in thisapplication, IGHD-derived amino acids (i.e., DH segments) are numberedbeginning with position 97, followed by positions 97A, 97B, etc. In thecurrently exemplified embodiment of the library, the shortest DH segmenthas three amino acids: 97, 97A and 97B, while the longest DH segment has10 amino acids: 97, 97A, 97B, 97C, 97D, 97E, 97F, 97G, 97H and 97I.

Example 5.2 Selection of the H3-JH Segments

There are six human germline IGHJ genes. During in vivo assembly ofantibody genes, these segments are progressively deleted at their 5′end. In this exemplary embodiment of the library, IGHJ gene segmentswith no deletions, or with 1, 2, 3, 4, 5, 6, or 7 deletions (at theamino acid level), yielding JH segments as short as 13 amino acids, wereincluded (Table 20). Other embodiments of the invention, in which theIGHJ gene segments are progressively deleted (at their 5′/N-terminalend) to yield 15, 14, 12, or 11 amino acids are also contemplated.

TABLE 20 IGHJ Gene Segments Selected  for use in the Exemplary LibraryIGHJ SEQ ID SEQ Segment [H3-JH]-[FRM4]¹ NO: H3-JH ID NO: JH1 parent AEYFQHWGQGTLVTVSS 253 AEYFQH 17 or JH1_1 JH1_2 EYFQHWGQGTLVTVSS 808EYFQH 830 JH1_3 YFQHWGQGTLVTVSS 809 YFQH 831 JH1_4 FQHWGQGTLVTVSS 810FQH JH1_5 QHWGQGTLVTVSS 811 QH JH2  YWYFDLWGRGTLVTVSS 254 YWYFDL 18parent  or JH2_1 JH2_2 WYFDLWGRGTLVTVSS 812 WYFDL 832 JH2_3YFDLWGRGTLVTVSS 813 YFDL 833 JH2_4 FDLWGRGTLVTVSS 814 FDL JH2_5DLWGRGTLVTVSS 815 DL JH3  AFDVWGQGTMVTVSS 255 AFDV 19 parent  or JH3_1JH3_2 FDVWGQGTMVTVSS 816 FDV JH3_3 DVWGQGTMVTVSS 817 DV JH4 YFDYWGQGTLVTVSS 256 YFDY 20 parent  or JH4_1 JH4_2 FDYWGQGTLVTVSS 818FDY JH4_3 DYWGQGTLVTVSS 819 DY JHS  NWFDSWGQGTLVTVSs 257 NWFDS 21parent  or JH5_1 JH5_2 WFDSWGQGTLVTVSs 820 WFDS 834 JH5_3 FDSWGQGTLVTVSS821 FDS JH5_4 DSWGQGTLVTVSS 822 DS JH6  YYYYYGMDVWGQGTTVTVSS 258YYYYYGMDV 22 parent  or JH6_1 JH6_2 YYYYGMDVWGQGTTVTVSS 823 YYYYGMDV 835JH6_3 YYYGMDVWGQGTTVTVSS 824 YYYGMDV 836 JH6_4 YYGMDVWGQGTTVTVSS 825YYGMDV 837 JH6_5 YGMDVWGQGTTVTVSS 826 YGMDV 838 JH6_6 GMDVWGQGTTVTVSS827 GMDV 839 JH6_7 MDVWGQGTTVTVSS 828 MDV JH6_8 DVWGQGTMVTVSS 829 DV¹H3-JH is defined as the portion of the IGHJ segment included within theKabat definition of CDRH3; FRM4 is defined as the portion of the IGHJsegment encoding framework region four.

According to the CDRH3 numbering system of this application, thecontribution of, for example, JH6_(—)1 to CDRH3, would be designated bypositions 99F, 99E, 99D, 99C, 99B, 99A, 100, 101 and 102 (Y, Y, Y, Y, Y,G, M, D and V, respectively). Similarly, the JH4_(—)3 sequence wouldcontribute amino acid positions 101 and 102 (D and Y, respectively) toCDRH3. However, in all cases of the exemplified library, the JH segmentwill contribute amino acids 103 to 113 to the FRM4 region, in accordancewith the standard Kabat numbering system for antibody variable regions(Kabat, op. cit. 1991). This may not be the case in other embodiments ofthe library.

Example 5.3 Selection of the N1 and N2 Segments

While the consideration of V-D-J recombination enhanced by mimicry ofthe naturally occurring process of progressive deletion (as exemplifiedabove) can generate enormous diversity, the diversity of the CDRH3sequences in vivo is further amplified by non-templated addition of avarying number of nucleotides at the V-D junction and the D-J junction.

N1 and N2 segments located at the V-D and D-J junctions, respectively,were identified in a sample containing about 2,700 antibody sequences(Jackson et al., J. Immunol. Methods, 2007, 324: 26) also analyzed bythe SoDA method of Volpe et al., Bioinformatics, 2006, 22: 438-44; (bothJackson et al., and Volpe et al., are incorporated by reference in theirentireties). Examination of these sequences revealed patterns in thelength and composition of N1 and N2. For the construction of thecurrently exemplified CDRH3 library, specific short amino acid sequenceswere derived from the above analysis and used to generate a number of N1and N2 segments that were incorporated into the CDRH3 design, using thesynthetic scheme described herein.

As described in the Detailed Description, certain embodiments of theinvention include N1 and N2 segments with rationally designed length andcomposition, informed by statistical biases in these parameters that arefound by comparing naturally occurring N1 and N2 segments in humanantibodies. According to data compiled from human databases (see, e.g.,Jackson et al., J. Immunol. Methods, 2007, 324: 26, incorporated byreference in its entirety), there are an average of about 3.02 aminoacid insertions for N1 and about 2.4 amino acid insertions for N2, nottaking into account insertions of two nucleotides or less. FIG. 2 showsthe length distributions of the N1 and N2 regions in human antibodies.In this exemplary embodiment of the invention, N1 and N2 were fixed to alength of 0, 1, 2, or 3 amino acids. The naturally occurring compositionof these sequences in human antibodies was used as a guide for theinclusion of different amino acid residues.

The naturally occurring composition of single amino acid, two aminoacids, and three amino acids N1 additions is defined in Table 21, andthe naturally occurring composition of the corresponding N2 additions isdefined in Table 22. The most frequently occurring duplets in the N1 andN2 set are compiled in Table 23.

TABLE 21 Composition of Naturally Occurring 1, 2, and 3 Amino Acid N1Additions* Number of Position Number of Position Number of Position 1Occurrences 2 Occurrences 3 Occurrences R 251 G 97 G 101 G 249 P 67 R 66P 173 R 67 P 47 L 130 S 42 S 47 S 117 L 39 L 38 A 84 V 33 A 33 V 62 E 24V 28 K 61 A 21 T 27 I 55 D 18 E 24 Q 51 I 18 D 22 T 51 T 18 K 18 D 50 K16 F 14 E 49 Y 16 I 13 F 3 H 13 W 13 H 32 F 12 N 10 N 30 Q 11 Y 10 W 28N 5 H 8 Y 21 W 5 Q 5 M 16 C 4 C 3 C 3 M 4 M 3 1546 530 530 *Defined asthe sequence C-terminal to “CARX” (SEQ ID NO: 840), or equivalent, ofVH, wherein “X” is the “tail” (e.g., D, E, G, or no amino acid residue).

TABLE 22 Composition of Naturally Occurring 1, 2, and 3 Amino Acid N2Additions* Number of Position Number of Position Number of Position 1Occurrences 2 Occurrences 3 Occurrences G 242 G 244 G 156 P 219 P 138 P79 R 180 R 86 S 54 L 132 S 85 R 51 S 123 T 77 L 49 A 97 L 74 A 41 T 78 A69 T 31 V 75 V 46 V 29 E 57 E 41 D 23 D 56 Y 38 E 23 F 54 D 36 W 23 H 54K 30 Q 19 Q 53 F 29 F 17 I 49 W 27 Y 17 N 45 H 24 H 16 Y 40 I 23 I 11 K35 Q 23 K 11 W 29 N 21 N 8 M 20 M 8 C 6 C 6 C 5 M 6 1644 1124 670*Defined as the sequence C-terminal to the D segment but not encoded byIGHJ genes.

TABLE 23 Top Twenty-Five Naturally Occurring N1 and N2 Duplets Number ofCumulative Individual Sequence Occurrences Frequency Frequency GG 170.037 0.037 PG 15 0.070 0.033 RG 15 0.103 0.033 PP 13 0.132 0.029 GP 120.158 0.026 GL 11 0.182 0.024 PT 10 0.204 0.022 TG 10 0.226 0.022 GV 90.246 0.020 RR 9 0.266 0.020 SG 8 0.284 0.018 RP 7 0.299 0.015 IG 60.312 0.013 GS 6 0.325 0.013 SR 6 0.338 0.013 PA 6 0.352 0.013 LP 60.365 0.013 VG 6 0.378 0.013 KG 6 0.389 0.011 GW 5 0.400 0.011 FP 50.411 0.011 LG 5 0.422 0.011 RS 5 0.433 0.011 TP 5 0.444 0.011 EG 50.455 0.011

Example 5.3.1 Selection of the N1 Segments

Analysis of the identified N1 segments, located at the junction betweenV and D, revealed that the eight most frequently occurring amino acidresidues were G, R, S, P, L, A, T and V (Table 21). The number of aminoacid additions in the N1 segment was frequently none, one, two, or three(FIG. 2). The addition of four or more amino acids was relatively rare.Therefore, in the currently exemplified embodiment of the library, theN1 segments were designed to include zero, one, two or three aminoacids. However, in other embodiments, N1 segments of four, five, or moreamino acids may also be utilized. G and P were always among the mostcommonly occurring amino acid residues in the N1 regions. Thus, in thepresent exemplary embodiment of the library, the N1 segments that aredipeptides are of the form GX, XG, PX, or XP, where X is any of theeight most commonly occurring amino acids listed above. Due to the factthat G residues were observed more frequently than P residues, thetripeptide members of the exemplary N1 library have the form GXG, GGX,or XGG, where X is, again, one of the eight most frequently occurringamino acid residues listed above. The resulting set of N1 sequences usedin the present exemplary embodiment of the library, include the “zero”addition amounts to 59 sequences, which are listed in Table 24.

TABLE 24 N1 Sequences Selected for Inclusion in the Exemplary LibrarySegment Type Sequences Number “Zero” (no addition) V segment joinsdirectly to D segment 1 Monomers G, P, R, A, S, L, T, V 8 Dimers GG, GP,GR, GA, GS, GL, GT, GV, PG, RG, AG, 28 SG, LG, TG, VG, PP, PR, PA, PS,PL, PT, PV, RP, AP, SP, LP, TP, VP Trimers GGG, GPG, GRG, GAG, GSG, GLG,GTG, GVG, 22 PGG, RGG, AGG, SGG, LGG, TGG, VGG, GGP, GGR, GGA, GGS, GGL,GGT, GGV

In accordance with the CDRH3 numbering system of the application, thesequences enumerated in Table 24 contribute the following positions toCDRH3: the monomers contribute position 96, the dimers to 96 and 96A,and the trimers to 96, 96A and 96B. In alternative embodiments, wheretetramers and longer segments could be included among the N1 sequences,the corresponding numbers would go on to include 96C, and so on.

Example 5.3.2 Selection of the N2 Segments

Similarly, analysis of the identified N2 segments, located at thejunction between D and J, revealed that the eight most frequentlyoccurring amino acid residues were also G, R, S, P, L, A, T and V (Table22). The number of amino acid additions in the N2 segment was alsofrequently none, one, two, or three (FIG. 2). For the design of the N2segments in the exemplary library, an expanded set of sequences wasutilized. Specifically, the sequences in Table 25 were used, in additionto the 59 sequences enumerated in Table 24, for N1.

TABLE 25 Extra Sequences in N2 Additions Segment Number Number TypeSequence New Total Monomers D, E, F, H, I, K, M, Q, W, Y 10 18 DimersAR, AS, AT, AY, DL, DT, EA, EK, FH, 54 82 FS, HL, HW, IS, KV, LD, LE,LR, LS, LT, NR, NT, QE, QL, QT, RA, RD, RE, RF, RH, RL, RR, RS, RV, SA,SD, SE, SF, SI, SK, SL, SQ, SR, SS, ST, SV, TA, TR, TS, TT, TW, VD, VS,WS, YS Trimers AAE, AYH, DTL, EKR, ISR, NTP, 18 40 PKS, PRP, PTA, PTQ,REL, RPL, SAA, SAL, SGL, SSE, TGL, WGT

The presently exemplified embodiment of the library, therefore, contains141 total N2 sequences, including the “zero” state. One of ordinaryskill in the art will readily recognize that these 141 sequences mayalso be used in the N1 region, and that such embodiments are within thescope of the invention. In addition, the length and compositionaldiversity of the N1 and N2 sequences can be further increased byutilizing amino acids that occur less frequently than G, R, S, P, L, A,T and V, in the N1 and N2 regions of naturally occurring antibodies, andincluding N1 and N2 segments of four, five, or more amino acids in thelibrary. Tables 21 to 23 and FIG. 2 provides information about thecomposition and length of the N1 and N2 sequences in naturally occurringantibodies that is useful for the design of additional N1 and N2 regionswhich mimic the natural composition and length.

In accordance with the CDRH3 numbering system of the application, N2sequences will begin at position 98 (when present) and extend to 98A(dimers) and 98B (trimers). Alternative embodiments may occupy positions98C, 98D, and so on.

Example 5.4 A CDRH3 Library

When the “tail” (i.e., G/D/E/-) is considered, the CDRH3 in theexemplified library may be represented by the general formula:

[G/D/E/-]-[N1]-[DH]-[N2]-[H3-JH]

In the currently exemplified, non-limiting, embodiment of the library,[G/D/E/-] represents each of the four possible terminal amino acid“tails”; N1 can be any of the 59 sequences in Table 24; DH can be any ofthe 278 sequences in Table 18; N2 can be any of the 141 sequences inTables 24 and 25; and H3-JH can be any of the 28 H3-JH sequences inTable 20. The total theoretical diversity or repertoire size of thisCDRH3 library is obtained by multiplying the variations at each of thecomponents, i.e., 4×59×278×141×28=2.59×10⁸.

However, as described in the previous examples, redundancies may beeliminated from the library. In the presently exemplified embodiment,the tail and N1 segments were combined, and redundancies were removedfrom the library. For example, considering the VH chassis, tail, and N1regions, the sequence [VH_Chassis]-[G] may be obtained in two differentways: [VH_Chassis]+[G]+[nothing] or [VH_Chassis]+[nothing]+[G]. Removalof redundant sequences resulted in a total of 212 unique [G/D/E/-]-[N1]segments out of the 236 possible combinations (i.e., 4 tails x 59 N1).Therefore, the actual diversity of the presently exemplified CDRH3library is 212×278×141×28=2.11×10⁸. FIG. 23 depicts the frequency ofoccurrence of different CDRH3 lengths in this library, versus thepreimmune repertoire of Lee et al.

Table 26 further illustrates specific exemplary sequences from the CDRH3library described above, using the CDRH3 numbering system of the presentapplication. In instances where a position is not used, the hyphensymbol (−) is included in the table instead.

TABLE 26 Examples of Designed CDRH3 Sequences According to the LibraryExemplified in Examples 1 to 5 [Tail] [N1] [DH] [N2] 95 96 96A 96B 9797A 97B 97C 97D 97E 97F 97G 97H 97I 98 98A 98B No. 1 G — — — Y Y Y — — —— — — — — — — No. 2 D G — — G Y C S G G S C Y S Y — — No. 3 E R — — I TI F G V — — — — G G — No. 4 — P P — V L L W F G E L L — D — — No. 5 G GS G Y Y Y G S G S Y Y N P — — No. 6 D — — — R G V I I — — — — — M — —No. 7 E S G — Y Y Y D S S G Y Y Y T G L No. 8 — S — — D Y G D Y — — — —— S I — No. 9 — P G — W F G — — — — — — — P S — No. 10 — — — — C S G G SC — — — — A Y — [H3-JH] CDRH3 99E 99D 99C 99B 99A 99 100 101 102 LengthNo. 1 — — — — — — — D V  6 No. 2 — — — — — F Q H 16 No. 3 — — — — — Y FD Y 14 No. 4 — — — — — — — D L 14 No. 5 — — — A E Y F Q H 21 No. 6 Y Y YY Y G M D V 16 No. 7 — — — — W Y F D L 21 No. 8 — — — — — — F D I 11 No.9 — — — Y Y G M D V 13 No. 10 — — — — N W F D P 13 Sequence Identifiers:No. 1 (SEQ ID NO: 542); No. 2 (SEQ ID NO: 543); No. 3 (SEQ ID NO: 544);No. 4 (SEQ ID NO: 545); No. 5 (SEQ ID NO: 546); No. 6 (SEQ ID NO: 547);No. 7 (SEQ ID NO: 548); No. 8 (SEQ ID NO: 549); No. 9 (SEQ ID NO: 550);No. 10 (SEQ ID NO: 551).

Example 6 Design of VKCDR3 Libraries

This example describes the design of a number of exemplary VKCDR3libraries. As specified in the Detailed Description, the actualversion(s) of the VKCDR3 library made or used in particular embodimentsof the invention will depend on the objectives for the use of thelibrary. In this example the Kabat numbering system for light chainvariable regions was used.

In order to facilitate examination of patterns of occurrence, humankappa light chain sequences were obtained from the publicly availableNCBI database (Appendix A). As for the heavy chain sequences (Example2), each of the sequences obtained from the publicly available databasewas assigned to its closest germline gene, on the basis of sequenceidentity. The amino acid compositions at each position were thendetermined within each kappa light chain subset.

Example 6.1 A Minimalist VKCDR3 Library

This example describes the design of a “minimalist” VKCDR3 library,wherein the VKCDR3 repertoire is restricted to a length of nineresidues. Examination of the VKCDR3 lengths of human sequences showsthat a dominant proportion (over 70%) has nine amino acids within theKabat definition of CDRL3: positions 89 through 97. Thus, the currentlyexemplified minimalist design considers only VKCDR3 of length nine.Examination of human kappa light chain sequences shows that there arenot strong biases in the usage of IGKJ genes; there are five such IKJgenes in humans. Table 27 depicts IGKJ gene usage amongst three datasets, namely Juul et al. (Clin. Exp. Immunol., 1997, 109: 194,incorporated by reference in its entirety), Klein and Zachau (Eur. J.Immunol., 1993, 23: 3248, incorporated by reference in its entirety),and the kappa light chain data set provided in Appendix A (labeled LUA).

TABLE 27 IGKJ Gene Usage in Various Data Sets Gene Klein Juul LUA IGKJ135.0% 29.0% 29.3% IGKJ2 25.0% 23.0% 24.1% IGKJ3 7.0% 8.0% 12.1% IGKJ426.0% 24.0% 26.5% IGKJ5 6.0% 18.0% 8.0%

Thus, a simple combinatorial of “M” VK chassis and the 5 IGKJ geneswould generate a library of size M×5. In the Kabat numbering system, forVKCDR3 of length nine, amino acid number 96 is the first encoded by theIGKJ gene. Examination of the amino acid occupying this position inhuman sequences showed that the seven most common residues are L, Y, R,W, F, P, and I, cumulatively accounting for about 85% of the residuesfound in position 96. The remaining 13 amino acids account for the other15%. The occurrence of all 20 amino acids at position 96 is presented inTable 28.

TABLE 28 Occurrence of 20 Amino Acid Residues at Position 96 in Human VKData Set Type Number Percent Cumulative L 333 22.3 22.3 Y 235 15.8 38.1R 222 14.9 52.9 W 157 10.5 63.5 F 148 9.9 73.4 I 96 6.4 79.8 P 90 6.085.9 Q 53 3.6 89.4 N 39 2.6 92.0 H 31 2.1 94.1 V 21 1.4 95.5 G 20 1.396.8 C 14 0.9 97.8 K 7 0.5 98.3 S 6 0.4 98.7 A 5 0.3 99.0 D 5 0.3 99.3 E5 0.3 99.7 T 5 0.3 100.0 M 0 0.0 100.0

To determine the origins of the seven residues most commonly found inposition 96, known human IGKJ amino acid sequences were examined (Table29).

TABLE 29 Known Human IGKJ Amino Acid Sequences Gene Sequence SEQ ID NO:IGKJ1 WTFGQGTKVEIK 552 IGKJ2 YTFGQGTKLEIK 553 IGKJ3 FTFGPGTKVDIK 554IGKJ4 LTFGGGTKVEIK 555 IGKJ5 ITFGQGTRLEIK 556

Without being bound by theory, five of the seven most commonly occurringamino acids found in position 96 of rearranged human sequences appear tooriginate from the first amino acid encoded by each of the five humanIGKJ genes, namely, W, Y, F, L, and I.

Less evident were the origins of the P and R residues. Without beingbound by theory, most of the human IGKV gene nucleotide sequences endwith the sequence CC, which occurs after (i.e., 3′ to) the end of thelast full codon (e.g., that encodes the C-terminal residue shown inTable 11). Therefore, regardless of which nucleotide is placed afterthis sequence (i.e., CCX, where X may be any nucleotide) the codon willencode a proline (P) residue. Thus, when the IGKJ gene undergoesprogressive deletion (just as in the IGHJ of the heavy chain; seeExample 5), the first full amino acid is lost and, if no deletions haveoccurred in the IGKV gene, a P residue will result.

To determine the origin of the arginine residue at position 96, theorigin of IGKJ genes in rearranged kappa light chain sequencescontaining R at position 96 were analyzed. The analysis indicated that Roccurred most frequently at position 96 when the IGKJ gene was IGKJ1(SEQ ID NO: 552). The germline W (position 1; Table 29) for IGKJ1 (SEQID NO: 552) is encoded by TGG. Without being bound by theory, a singlenucleotide change of T to C (yielding CGG) or A (yielding AGG) will,therefore, result in codons encoding Arg (R). A change to G (yieldingGGG) results in a codon encoding Gly (G). R occurs about ten times moreoften at position 96 in human sequences than G (when the IGKJ gene isIGKJ1 (SEQ ID NO: 552)), and it is encoded by CGG more often than AGG.Therefore, without being bound by theory, C may originate from one ofthe aforementioned two Cs at the end of IGKV gene. However, regardlessof the mechanism(s) of occurrence, R and P are among the most frequentlyobserved amino acid types at position 96, when the length of VKCDR3 is9. Therefore, a minimalist VKCDR3 library may be represented by thefollowing amino acid sequence:

[VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[TFGGGTKVEIK(SEQ ID NO:841)]

In this sequence, VK_Chassis represents any selected VK chassis (fornon-limiting examples, see Table 11), specifically Kabat residues 1 to88 encoded by the IGKV gene. L3-VK represents the portion of the VKCDR3encoded by the chosen IGKV gene (in this embodiment, residues 89-95).F/L/I/R/W/Y/P represents any one of amino residues F, L, I, R, W, Y, orP. In this exemplary representation, IKJ4 (minus the first residue) hasbeen depicted. Without being bound by theory, apart from IGKJ4 (SEQ IDNO: 555) being among the most commonly used IGKJ genes in humans, theGGG amino acid sequence is expected to lead to larger conformationalflexibility than any of the alternative IGKJ genes, which contain a GXGamino acid sequence, where X is an amino acid other than G. In someembodiments, it may be advantageous to produce a minimalist pre-immunerepertoire with a higher degree of conformational flexibility.Considering the ten VK chassis depicted in Table 11, one implementationof the minimalist VKCDR3 library would have 70 members resulting fromthe combination of 10 VK chassis by 7 junction (position 96) options andone IGKJ-derived sequence (e.g., IGKJ4 (SEQ ID NO: 555)). Although thisembodiment of the library has been depicted using IGKJ4 (SEQ ID NO:555), it is possible to design a minimalist VKCDR3 library using one ofthe other four IGKJ sequences. For example, another embodiment of thelibrary may have 350 members (10 VK chassis by 7 junctions by 5 IGKJgenes).

One of ordinary skill in the art will readily recognize that one or moreminimalist VKCDR3 libraries may be constructed using any of the IGKJgenes. Using the notation above, these minimalist VKCDR3 libraries mayhave sequences represented by, for example:

JK1: [VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[TFGQGTKVEIK(SEQ ID NO: 528)];

JK2: [VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[TFGQGTKLEIK(SEQ ID NO: 842];

JK3: [VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[TFGPGTKVDIK(SEQ ID NO: 843];and

JK5: [VK_Chassis]-[L3-VK]-[F/L/I/R/W/Y/P]-[TFGQGTRLEIK(SEQ ID NO: 844].

Example 6.2 A VKCDR3 Library of About 10⁵ Complexity

In this example, the nine residue VKCDR3 repertoire described in Example6.1 is expanded to include VKCDR3 lengths of eight and ten residues.Moreover, while the previously enumerated VKCDR3 library included the VKchassis and portions of the IGKJ gene not contributing to VKCDR3, thepresently exemplified version focuses only on residues comprising aportion of VKCDR3. This embodiment may be favored, for example, whenrecombination with a vector which already contains VK chassis sequencesand constant region sequences is desired.

While the dominant length of VKCDR3 sequences in humans is nine aminoacids, other lengths appear at measurable rates that cumulativelyapproach almost 30% of kappa light chain sequences. In particular,VKCDR3 of lengths 8 and 10 represent, respectively, about 8.5% and about16% of sequences in representative samples (FIG. 3). Thus, a morecomplex VKCDR3 library includes CDR lengths of 8 to 10 amino acids; thislibrary accounts for over 95% of the length distribution observed intypical collections of human VKCDR3 sequences. This library also enablesthe inclusion of additional variation outside of the junction betweenthe VK and JK genes. The present example describes such a library. Thelibrary comprises 10 sub-libraries, each designed around one of the 10exemplary VK chassis depicted in Table 11. Clearly, the approachexemplified here can be generalized to consider M different chassis,where M may be less than or more than 10.

To characterize the variability within the polypeptide segment occupyingKabat positions 89 to 95, human kappa light chain sequence collectionsderived from each of the ten germline sequences of Example 3 werealigned and compared separately (i.e., within the germline group). Thisanalysis enabled us to discern the patterns of sequence variation ateach individual position in each kappa light chain sequence, grouped bygermline. The table below shows the results for sequences derived fromIGKV1-39 (SEQ ID NO: 233).

TABLE 30 Percent Occurrence of Amino Acid Types in IGKV1-39-DerivedSequences Amino Acid P89 P90 P91 P92 P93 P94 P95 A 0 0 1 0 0 4 1 C 0 0 00 0 0 0 D 0 0 1 1 3 0 0 E 0 1 0 0 0 0 0 F 0 0 0 5 0 2 0 G 0 0 2 1 2 0 0H 1 1 0 4 0 0 0 I 0 0 1 0 4 5 1 K 0 0 0 1 2 0 0 L 3 0 0 1 1 3 7 M 0 0 00 0 1 0 N 0 0 3 2 6 2 0 P 0 0 0 0 0 4 85 Q 96 97 0 0 0 0 0 R 0 0 0 0 5 02 S 0 0 80 4 65 6 3 T 0 0 9 0 10 65 1 V 0 0 0 0 0 1 1 W 0 0 0 0 0 0 0 Y0 0 2 80 0 3 0

For example, at position 89, two amino acids, Q and L, account for about99% of the observed variability, and thus in the currently exemplifiedlibrary (see below), only Q and L were included in position 89. Inlarger libraries, of course, additional, less frequently occurring aminoacid types (e.g., H), may also be included.

Similarly, at position 93 there is more variation, with amino acid typesS, T, N, R and I being among the most frequently occurring. Thecurrently exemplified library thus aimed to include these five aminoacids at position 93, although clearly others could be included in morediverse libraries. However, because this library was constructed viastandard chemical oligonucleotide synthesis, one is bound by the limitsof the genetic code, so that the actual amino acid set represented atposition 93 of the exemplified library consists of S, T, N, R, P and H,with P and H replacing I (see exemplary 9 residue VKCDR3 in Table 32,below). This limitation may be overcome by using codon-based synthesisof oligonucleotides, as described in Example 6.3, below. A similarapproach was followed at the other positions and for the othersequences: analysis of occurrences of amino acid type per position,choice from among most frequently occurring subset, followed byadjustment as dictated by the genetic code.

As indicated above, the library employs a practical and facile synthesisapproach using standard oligonucleotide synthesis instrumentation anddegenerate oligonucleotides. To facilitate description of the library,the IUPAC code for degenerate nucleotides, as given in Table 31, will beused.

TABLE 31 Degenerate Base Symbol Definition IUPAC Symbol Base PairComposition A A (100%) C C (100%) G G (100%) T T (100%) R A (50%) G(50%) Y C (50%) T (50%) W A (50%) T (50%) S C (50%) G (50%) M A (50%) C(50%) K G (50%) T (50%) B C (33%) G (33%) T (33%) (*) D A (33%) G (33%)T (33%) H A (33%) C (33%) T (33%) V A (33%) C (33%) G (33%) N A (25%) C(25%) G (25%) T (25%) (*) 33% is short hand here for 1/3 (i.e., 33.3333. . . %)

Using the VK1-39 chassis with VKCDR3 of length nine as an example, theVKCDR3 library may be represented by the following four oligonucleotides(left column in Table 32), with the corresponding amino acids encoded ateach position of CDRL3 (Kabat numbering) provided in the columns on theright.

TABLE 32 Exemplary Oligonucleotides  Encoding a VK1-39 CDR3 LibraryOligonucleotide Sequence 89 90 91 92 93 94 95 95A 96 97CWGSAAWCATHCMVTABTCCTTWCACT LQ EQ ST FSY HNPRST IST P — FY T(SEQ ID NO: 307) CWGSAAWCATHCMVTABTCCTMTCACT LQ EQ ST FSY HNPRST IST P —IL T (SEQ ID NO: 308) CWGSAAWCATHCMVTABTCCTWGGACT LQ EQ ST FSY HNPRSTIST P — WR T (SEQ ID NO: 309) CWGSAAWCATHCMVTABTCCTCBTACT LQ EQ ST FSYHNPRST IST P PLR — T (SEQ ID NO: 310)

For example, the first codon (CWG) of the first nucleotide of Table 32,corresponding to Kabat position 89, represents 50% CTG and 50% CAG,which encode Leu (L) and Gln (Q), respectively. Thus, the expressedpolypeptide would be expected to have L and Q each about 50% of thetime. Similarly, for Kabat position 95A of the fourth oligonucleotide,the codon CBT represents ⅓ each of CCT, CGT and CTT, corresponding inturn to ⅓ each of Pro (P), Leu (L) and Arg (R) upon translation. Bymultiplying the number of options available at each position of thepeptide sequence, one can obtain the complexity, in peptide space,contributed by each oligonucleotide. For the VK1-39 example above, thenumbers are 864 for the first three oligonucleotides and 1,296 for thefourth oligonucleotide. Thus, the oligonucleotides encoding VK1-39 CDR3sof length nine contribute 3,888 members to the library. However, asshown in Table 32, sequences with L or R at position 95A (when position96 is empty) are identical to those with L or R at position 96 (and 95Aempty). Therefore, the 3,888 number overestimates the LR contributionand the actual number of unique members is slightly lower, at 3,024. Asdepicted in Table 33, for the complete list of oligonucleotides thatrepresent VKCDR3 of sizes 8, 9, and 10, for all 10 VK chassis, theoverall complexity is about 1.3×10⁵ or 1.2×10⁵ unique sequences aftercorrecting for over-counting of the LR contribution for the size 9VKCDR3.

TABLE 33Degenerate Oligonucleotides Encoding an Exemplary VKCDR3 Library Junc-tion Degenerate SEQ CDRL3 Type Oligonu- ID Chassis Length (1) cleotideNO: 89 90 91 92 93 94 95 95A 96 97 VK1-5 8 1  CASCASTM 259 HQ  HQ SYDGHNRS AGST FY — — FY T CVRTRSTT WCTWCACT VK1-5 8 2  CASCASTM 260 HQ  HQSY DGHNRS AGST FY — — IL T CVRTRSTT WCMTCACT VK1-5 8 3  CASCASTM 261 HQ HQ SY DGHNRS AGST FY — — WR T CVRTRSTT WCWGGACT VK1-5 8 4  CASCASTM 262HQ  HQ SY DGHNRS AGST FY PS — — T CVRTRSTT WCYCTACT VK1-5 9 1  CASCASTM263 HQ  HQ SY DGHNRS AGST FY PS — FY T CVRTRSTT WCYCTTWC ACT VK1-5 9 2CASCASTM 264 HQ  HQ SY DGHNRS AGST FY PS — IL T CVRTRSTT WCYCTMTC ACTVK1-5 9 3  CASCASTM 265 HQ  HQ SY DGHNRS AGST FY PS — WR T CVRTRSTTWCYCTWGG ACT VK1-5 9 4  CASCASTM 266 HQ  HQ SY DGHNRS AGST FY PS PS — TCVRTRSTT WCYCTYCT ACT VK1-5 10 1  CASCASTM 267 HQ  HQ SY DGHNRS AGST FYPS PLR FY T CVRTRSTT WCYCTCBT TWCACT VK1-5 10 2  CASCASTM 268 HQ  HQ SYDGHNRS AGST FY PS PLR IL T CVRTRSTT WCYCTCBT MTCACT VK1-5 10 3  CASCASTM269 HQ  HQ SY DGHNRS AGST FY PS PLR WR T CVRTRSTT WCYCTCBT WGGACT VK1-128 1  CASCASDC 270 HQ  HQ AST ADGNST NS FL — — FY T TRVCARTT TSTWCACTVK1-12 8 2  CASCASDC 271 HQ  HQ AST ADGNST NS FL — — IL T TRVCARTTTSMTCACT VK1-12 8 3  CASCASDC 272 HQ  HQ AST ADGNST NS FL — — WR TTRVCARTT TSWGGACT VK1-12 8 4  CASCASDC 273 HQ  HQ AST ADGNST NS FL P — —T TRVCARTT TSCCTACT VK1-12 9 1  CASCASDC 274 HQ  HQ AST ADGNST NS FL P —FY T TRVCARTT TSCCTTWC ACT VK1-12 9 2  CASCASDC 275 HQ  HQ AST ADGNST NSFL P — IL T TRVCARTT TSCCTMTC ACT VK1-12 9 3  CASCASDC 276 HQ  HQ ASTADGNST NS FL P — WR T TRVCARTT TSCCTWGG ACT VK1-12 9 4  CASCASDC 277 HQ HQ AST ADGNST NS FL P PLR — T TRVCARTT TSCCTCBT ACT VK1-12 10 1 CASCASDC 278 HQ  HQ AST ADGNST NS FL P PLR FY T TRVCARTT TSCCTCBT TWCACTVK1-12 10 2  CASCASDC 279 HQ  HQ AST ADGNST NS FL P PLR IL T TRVCARTTTSCCTCBT MTCACT VK1-12 10 3  CASCASDC 280 HQ  HQ AST ADGNST NS FL P PLRWR T TRVCARTT TSCCTCBT WGGACT VK1-27 8 1  CASMAGTW 281 HQ  KQ FY DGNSRST AGV  — — FY T CRRTASKG BATWCACT VK1-27 8 2  CASMAGTW 282 HQ  KQ FYDGNS RST AGV  — — IL T CRRTASKG BAMTCACT VK1-27 8 3  CASMAGTW 283 HQ  KQFY DGNS RST AGV  — — WR T CRRTASKG BAWGGACT VK1-27 8 4  CASMAGTW 284 HQ KQ FY DGNS RST AGV  P — — T CRRTASKG BACCTACT VK1-27 9 1  CASMAGTW 285HQ  KQ FY DGNS RST AGV  P — FY T CRRTASKG BACCTTWC ACT VK1-27 9 2 CASMAGTW  286 HQ KQ FY DGNS RST AGV P — IL T CRRTASKG BACCTMTC ACTVK1-27 9 3  CASMAGTW 287 HQ  KQ FY DGNS RST AGV  P — WR T CRRTASKGBACCTWGG ACT VK1-27 9 4  CASMAGTW 288 HQ  KQ FY DGNS RST AGV  P PLR — TCRRTASKG BACCTCBT ACT VK1-27 10 1  CASMAGTW 289 HQ  KQ FY DGNS RST AGV P PLR FY T CRRTASKG BACCTCBT TWCACT VK1-27 10 2  CASMAGTW 290 HQ  KQ FYDGNS RST AGV  P PLR IL T CRRTASKG BACCTCBT MTCACT VK1-27 10 3  CASMAGTW291 HQ  KQ FY DGNS RST AGV  P PLR WR T CRRTASKG BACCTCBT WGGACT VK1-33 81  CASCWTTM 292 HQ  HL SY DN ADGNS DFH — — FY T CRATRVCB T LVY WTTWCACTVK1-33 8 2  CASCWTTM 293 HQ  HL SY DN ADGNS DFH — — IL T CRATRVCB T LVYWTMTCACT VK1-33 8 3  CASCWTTM 294 HQ  HL SY DN ADGNS DFH — — WR TCRATRVCB T LVY WTWGGACT VK1-33 8 4  CASCWTTM 295 HQ  HL SY DN ADGNS DFHP — — T CRATRVCB T LVY WTCCTACT VK1-33 9 1  CASCWTTM 296 HQ  HL SY DNADGNS DFH P — FY T CRATRVCB T LVY WTCCTTWC ACT VK1-33 9 2  CASCWTTM 297HQ  HL SY DN ADGNS DFH P — IL T CRATRVCB T LVY WTCCTMTC ACT VK1-33 9 3 CASCWTTM 298 HQ  HL SY DN ADGNS DFH P — WR T CRATRVCB T LVY WTCCTWGG ACTVK1-33 9 4  CASCWTTM 299 HQ  HL SY DN ADGNS DFH P PLR — T CRATRVCB T LVYWTCCTCBT ACT VK1-33 10 1  CASCWTTM 300 HQ  HL SY DN ADGNS DFH P PLR FY TCRATRVCB T LVY WTCCTCBT TWCACT VK1-33 10 2  CASCWTTM 301 HQ  HL SY DNADGNS DFH P PLR IL T CRATRVCB T LVY WTCCTCBT MTCACT VK1-33 10 3 CASCWTTM 302 HQ  HL SY DN ADGNS DFH P PLR WR T CRATRVCB T LVY WTCCTCBTWGGACT VK1-39 8 1  CWGSAAWC 303 LQ  EQ ST FSY HNPRS IST  — — FY TATHCMVTA T BTTWCACT VK1-39 8 2  CWGSAAWC 304 LQ  EQ ST FSY HNPRS IST  —— IL T ATHCMVTA T BTMTCACT VK1-39 8 3  CWGSAAWC 305 LQ  EQ ST FSY HNPRSIST  — — WR T ATHCMVTA T BTWGGACT VK1-39 8 4  CWGSAAWC 306 LQ  EQ ST FSYHNPRS IST  P — — T ATHCMVTA T BTCCTACT VK1-39 9 1  CWGSAAWC 307 LQ  EQST FSY HNPRS IST  P — FY T ATHCMVTA T BTCCTTWC ACT VK1-39 9 2  CWGSAAWC308 LQ  EQ ST FSY HNPRS IST  P — IL T ATHCMVTA T BTCCTMTC ACT VK1-39 93  CWGSAAWC 309 LQ  EQ ST FSY HNPRS IST  P — WR T ATHCMVTA T BTCCTWGGACT VK1-39 9 4  CWGSAAWC 310 LQ  EQ ST FSY HNPRS IST  P PLR — T ATHCMVTAT BTCCTCBT ACT VK1-39 10 1  CWGSAAWC 311 LQ  EQ ST FSY HNPRS IST  P PLRFY T ATHCMVTA T BTCCTCBT TWCACT VK1-39 10 2  CWGSAAWC 312 LQ  EQ ST FSYHNPRS IST  P PLR IL T ATHCMVTA T BTCCTCBT MTCACT VK1-39 10 3  CWGSAAWC313 LQ  EQ ST FSY HNPRS IST  P PLR WR T ATHCMVTA T BTCCTCBT WGGACTVK3-11 8 1  CASCASAG 314 HQ  HQ RS GRS ADGNS SW — — FY T WRGKRVCT TSGTWCACT VK3-11 8 2  CASCASAG 315 HQ  HQ RS GRS ADGNS SW — — IL TWRGKRVCT T SGMTCACT VK3-11 8 3  CASCASAG 316 HQ  HQ RS GRS ADGNS SW — —WR T WRGKRVCT T SGWGGACT VK3-11 8 4  CASCASAG 317 HQ  HQ RS GRS ADGNS SWP — — T WRGKRVCT T SGCCTACT VK3-11 9 1  CASCASAG 318 HQ  HQ RS GRS ADGNSSW P — FY T WRGKRVCT T SGCCTTWC ACT VK3-11 9 2  CASCASAG 319 HQ  HQ RSGRS ADGNS SW P — IL T WRGKRVCT T SGCCTMTC ACT VK3-11 9 3  CASCASAG 320HQ  HQ RS GRS ADGNS SW P — WR T WRGKRVCT T SGCCTWGG ACT VK3-11 9 4 CASCASAG 321 HQ  HQ RS GRS ADGNS SW P PLR — T WRGKRVCT T SGCCTCBT ACTVK3-11 10 1  CASCASAG 322 HQ  HQ RS GRS ADGNS SW P PLR FY T WRGKRVCT TSGCCTCBT TWCACT VK3-11 10 2  CASCASAG 323 HQ  HQ RS GRS ADGNS SW P PLRIL T WRGKRVCT T SGCCTCBT MTCACT VK3-11 10 3  CASCASAG 324 HQ  HQ RS GRSADGNS SW P PLR WR T WRGKRVCT T SGCCTCBT WGGACT VK3-15 8 1  CASCASTM 325HQ  HQ SY DGHNRS DEGKN W — — FY T CVRTRRKT RS GGTWCACT VK3-15 8 2 CASCASTM 326 HQ  HQ SY DGHNRS DEGKN W — — IL T CVRTRRKT RS GGMTCACTVK3-15 8 3  CASCASTM 327 HQ  HQ SY DGHNRS DEGKN W — — WR T CVRTRRKT RSGGWGGACT VK3-15 8 4  CASCASTM 328 HQ  HQ SY DGHNRS DEGKN W P — — TCVRTRRKT RS GGCCTACT VK3-15 9 1  CASCASTM 329 HQ  HQ SY DGHNRS DEGKN W P— FY T CVRTRRKT RS GGCCTTWC ACT VK3-15 9 2  CASCASTM 330 HQ  HQ SYDGHNRS DEGKN W P — IL T CVRTRRKT RS GGCCTMTC ACT VK3-15 9 3  CASCASTM331 HQ  HQ SY DGHNRS DEGKN W P — WR T CVRTRRKT RS GGCCTWGG ACT VK3-15 94  CASCASTM 332 HQ  HQ SY DGHNRS DEGKN W P PLR — T CVRTRRKT RS GGCCTCBTACT VK3-15 10 1  CASCASTM 333 HQ  HQ SY DGHNRS DEGKN W P PLR FY TCVRTRRKT RS GGCCTCBT TWCACT VK3-15 10 2  CASCASTM 334 HQ  HQ SY DGHNRSDEGKN W P PLR IL T CVRTRRKT RS GGCCTCBT MTCACT VK3-15 10 3  CASCASTM 335HQ  HQ SY DGHNRS DEGKN W P PLR WR T CVRTRRKT RS GGCCTCBT WGGACT VK3-20 81  CASCASTW 336 HQ  HQ FY DG ADEGK AS — — FY T CGRTRVKK NRST CATWCACTVK3-20 8 2  CASCASTW 337 HQ  HQ FY DG ADEGK AS — — IL T CGRTRVKK NRSTCAMTCACT VK3-20 8 3  CASCASTW 338 HQ  HQ FY DG ADEGK AS — — WR TCGRTRVKK NRST CAWGGACT VK3-20 8 4  CASCASTW 339 HQ  HQ FY DG ADEGK AS P— — T CGRTRVKK NRST CACCTACT VK3-20 9 1  CASCASTW 340 HQ  HQ FY DG ADEGKAS P — FY T CGRTRVKK NRST CACCTTWC ACT VK3-20 9 2  CASCASTW 341 HQ  HQFY DG ADEGK AS P — IL T CGRTRVKK NRST CACCTMTC ACT VK3-20 9 3  CASCASTW342 HQ  HQ FY DG ADEGK AS P — WR T CGRTRVKK NRST CACCTWGG ACT VK3-20 94  CASCASTW 343 HQ  HQ FY DG ADEGK AS P PLR — T CGRTRVKK NRST CACCTCBTACT VK3-20 10 1  CASCASTW 344 HQ  HQ FY DG ADEGK AS P PLR FY T CGRTRVKKNRST CACCTCBT TWCACT VK3-20 10 2  CASCASTW 345 HQ  HQ FY DG ADEGK AS PPLR IL T CGRTRVKK NRST CACCTCBT MTCACT VK3-20 10 3  CASCASTW 346 HQ  HQFY DG ADEGK AS P PLR WR T CGRTRVKK NRST CACCTCBT WGGACT VK2-28 8 1 ATGCASRB 347 M HQ AGI LR DEHQ IST  — — FY T TCKTSASA STV BTTWCACT VK2-288 2  ATGCASRB 348 M HQ AGI LR DEHQ IST  — — IL T TCKTSASA STV BTMTCACTVK2-28 8 3  ATGCASRB 349 M HQ AGI LR DEHQ IST  — — WR T TCKTSASA STVBTWGGACT VK2-28 8 4  ATGCASRB 350 M HQ AGI LR DEHQ IST  P — — T TCKTSASASTV BTCCTACT VK2-28 9 1  ATGCASRB 351 M HQ AGI LR DEHQ IST  P — FY TTCKTSASA STV BTCCTTWC ACT VK2-28 9 2  ATGCASRB 352 M HQ AGI LR DEHQ IST P — IL T TCKTSASA STV BTCCTMTC ACT VK2-28 9 3  ATGCASRB 353 M HQ AGI LRDEHQ IST  P — WR T TCKTSASA STV BTCCTWGG ACT VK2-28 9 4  ATGCASRB 354 MHQ AGI LR DEHQ IST  P PLR — T TCKTSASA STV BTCCTCBT ACT VK2-28 10 1 ATGCASRB 355 M HQ AGI LR DEHQ IST  P PLR FY T TCKTSASA STV BTCCTCBTTWCACT VK2-28 10 2  ATGCASRB 356 M HQ AGI LR DEHQ IST  P PLR IL TTCKTSASA STV BTCCTCBT MTCACT VK2-28 10 3  ATGCASRB 357 M HQ AGI LR DEHQIST  P PLR WR T TCKTSASA STV BTCCTCBT WGGACT VK4-1 8 1  CASCASTW 358 HQ HQ FY FY ADGNS IST  — — FY T CTWCRVCA T BTTWCACT VK4-1 8 2  CASCASTW 359HQ  HQ FY FY ADGNS IST  — — IL T CTWCRVCA T BTMTCACT VK4-1 8 3  CASCASTW360 HQ  HQ FY FY ADGNS IST  — — WR T CTWCRVCA T BTWGGACT VK4-1 8 4 CASCASTW 361 HQ  HQ FY FY ADGNS IST  P — — T CTWCRVCA T BTCCTACT VK4-1 91  CASCASTW 362 HQ  HQ FY FY ADGNS IST  P — FY T CTWCRVCA T BTCCTTWC ACTVK4-1 9 2  CASCASTW 363 HQ  HQ FY FY ADGNS IST  P — IL T CTWCRVCA TBTCCTMTC ACT VK4-1 9 3  CASCASTW 364 HQ  HQ FY FY ADGNS IST  P — WR TCTWCRVCA T BTCCTWGG ACT VK4-1 9 4  CASCASTW 365 HQ  HQ FY FY ADGNS IST P PLR — T CTWCRVCA T BTCCTCBT ACT VK4-1 10 1  CASCASTW 366 HQ  HQ FY FYADGNS IST  P PLR FY T CTWCRVCA T BTCCTCBT TWCACT VK4-1 10 2  CASCASTW367 HQ  HQ FY FY ADGNS IST  P PLR IL T CTWCRVCA T BTCCTCBT MTCACT VK4-110 3  CASCASTW 368 HQ  HQ FY FY ADGNS IST  P PLR WR T [Alter- CTWCRVCA Tnative BTCCTCBT for  WGGACT VK1-33] (2) VK1-33 8 1  CASCWATM 369 HQ  QLSY DN ADGNS DFH — — FY T CRATRVCB T LVY WTTWCACT VK1-33 8 2  CASCWATM370 HQ  QL SY DN ADGNS DFH — — IL T CRATRVCB T LVY WTMTCACT VK1-33 8 3 CASCWATM 371 HQ  QL SY DN ADGNS DFH — — WR T CRATRVCB T LVY WTWGGACTVK1-33 8 4  CASCWATM 372 HQ  QL SY DN ADGNS DFH P — — T CRATRVCB T LVYWTCCTACT VK1-33 9 1  CASCWATM 373 HQ  QL SY DN ADGNS DFH P — FY TCRATRVCB T LVY WTCCTTWC ACT VK1-33 9 2  CASCWATM 374 HQ  QL SY DN ADGNSDFH P — IL T CRATRVCB T LVY WTCCTMTC ACT VK1-33 9 3  CASCWATM 375 HQ  QLSY DN ADGNS DFH P — WR T CRATRVCB T LVY WTCCTWGG ACT VK1-33 9 4 CASCWATM 376 HQ  QL SY DN ADGNS DFH P PLR — T CRATRVCB T LVY WTCCTCBTACT VK1-33 10 1  CASCWATM 377 HQ  QL SY DN ADGNS DFH P PLR FY T CRATRVCBT LVY WTCCTCBT TWCACT VK1-33 10 2  CASCWATM 378 HQ  QL SY DN ADGNS DFH PPLR IL T CRATRVCB T LVY WTCCTCBT MTCACT VK1-33 10 3  CASCWATM 379 HQ  QLSY DN ADGNS DFH P PLR WR T CRATRVCB T LVY WTCCTCBT WGGACT (1) Junctiontype 1 has position 96 as FY, type 2 as IL, type 3 as RW, and type 4 hasa deletion. (2) Two embodiments are shown for the VK1-33 library. In oneembodiment, the second codon was CWT. In another embodiment, it was CWAor CWG.

Example 6.3 More Complex VKCDR3 Libraries

This example demonstrates how a more faithful representation of aminoacid variation at each position may be obtained by using a codon-basedsynthesis approach (Virnekas et al. Nucleic Acids Res., 1994, 22: 5600).This synthetic scheme also allows for finer control of the proportionsof particular amino acids included at a position. For example, asdescribed above for the VK1-39 sequences, position 89 was designed as50% Q and 50% L; however, as Table 30 shows, Q is used much morefrequently than L. The more complex VKCDR3 libraries of the presentexample account for the different relative occurrence of Q and L, forexample, 90% Q and 10% L. Such control is better exercised withincodon-based synthetic schemes, especially when multiple amino acid typesare considered.

This example also describes an implementation of a codon-based syntheticscheme, using the ten VK chassis described in Table 11. Similarapproaches, of course, can be implemented with more or fewer suchchassis. As indicated in the Detailed Description, a unique aspect ofthe design of the present libraries, as well as those of the precedingexamples, is the germline or chassis-based aspect, which is meant topreserve more of the integrity and variation of actual human kappa lightchain sequences. This is in contrast to other codon-based synthesis ordegenerate oligonucleotide synthesis approaches that have been describedin the literature and that aim to produce “one-size-fits-all” (e.g.,consensus) kappa light chain libraries (e.g. Knappik, et al., J MolBiol, 2000, 296: 57; Akamatsu et al., J Immunol, 1993, 151: 4651).

With reference to Table 30, obtained for VK1-39, one can thus design thelength nine VKCDR3 library of Table 34. Here, for practical reasons, theproportions at each position are denoted in multiples of five percentagepoints. As better synthetic schemes are developed, finer resolution maybe obtained—for example to resolutions of one, two, three, or fourpercent.

TABLE 34 Amino Acid Composition (%) at Each VKCDR3 Position for VK1-39Library With CDR Length of Nine Residues Amino Acid 89 90 91 92 93 94 9596 (*) 97 (*) A 5 5 D 5 5 E 5 5 F 5 10 G 5 5 5 5 H 5 5 5 5 I 5 5 K 5 L10 5 10 20 M N 0 0 5 0 5 P 5 85 5 Q 85 90 5 R 5 5 10 S 80 5 60 5 5 T 1010 65 90 V 5 W 15 Y 5 75 5 15 Number 3 3 4 6 8 8 3 11 3 Different (*)The composition of positions 96 and 97, determined largely by junctionand IGKJ diversity, could be the same for length 9 VK CDR3 of allchassis.

The library of Table 34 would have 1.37×10⁶ unique polypeptidesequences, calculated by multiplying together the numbers in the bottomrow of the table.

The underlined 0 entries for Asn (N) at certain positions representregions where the possibility of having N-linked glycosylation sites inthe VKCDR3 has been minimized or eliminated. Peptide sequences with thepattern N-X-(S or T)-Z, where X and Z are different from P, may undergopost-translational modification in a number of expression systems,including yeast and mammalian cells. Moreover, the nature of suchmodification depends on the specific cell type and, even for a givencell type, on culture conditions. N-linked glycosylation may bedisadvantageous when it occurs in a region of the antibody moleculelikely to be involved in antigen binding (e.g., a CDR), as the functionof the antibody may then be influenced by factors that may be difficultto control. For example, considering position 91 above, one can observethat position 92 is never P. Position 94 is not P in 95% of the cases.However, position 93 is S or T in 75% (65+10) of the cases. Thus,allowing N at position 91 would generate the undesirable motifN—X-(T/S)-Z (with both X and Z distinct from P), and a zero occurrencehas therefore been implemented, even though N is observed with somefrequency in actual human sequences (see Table 30). A similar argumentapplies for N at positions 92 and 94. It should be appreciated, however,that if the antibody library were to be expressed in a system incapableof N-linked glycosylation, such as bacteria, or under culture conditionsin which N-linked glycosylation did not occur, this consideration maynot apply. However, even in the event that the organism used to expresslibraries with potential N-linked glycosylation sites is incapable ofN-linked glycosylation (e.g., bacteria), it may still be desirable toavoid N-X-(S/T) sequences, as the antibodies isolated from suchlibraries may be expressed in different systems (e.g., yeast, mammaliancells) later (e.g., toward clinical development), and the presence ofcarbohydrate moieties in the variable domains, and the CDRs inparticular, may lead to unwanted modifications of activity. Theseembodiments are also included within the scope of the invention. To ourknowledge, VKCDR3 libraries known in the art have not considered thiseffect, and thus a proportion of their members may have the undesirablequalities mentioned above.

We also designed additional sub-libraries, related to the libraryoutlined in Table 34, for VKCDR3 of lengths 8 and 10. In theseembodiments, the compositions at positions 89 to 94 and 97 remain thesame as those depicted in Table 34. Additional diversity, introduced atpositions 95 and 95A, the latter being defined for VKCDR3 of length 10only, are illustrated in Table 35.

TABLE 35 Amino Acid Composition (%) for VK1-39 Libraries of Lengths 8and 10 Position Position 95 - 95 - Position Length Length 95A - AminoAcid 8 (*) 10 (**) Length 10 A D E F 5 G 5 H I 10 5 K L 20 10 10 M N P25 85 60 Q R 10 5 10 S 5 5 T 5 V 5 W 10 Y 10 Number 9 3 8 Different (*)Position 96 is deleted in VKCDR3 of size 8. (**) This is the samecomposition as in VKCDR3 of size 9.

The total number of unique members in the VK1-39 library of length 8,thus, can be obtained as before, and is 3.73×10⁵ (or, 3×3×4×6×8×8×9×3).Similarly, the complexity of the VK1-39 library of length 10 would be10.9×10⁶ (or 8 times that of the library of size 9, as there isadditional 8-fold variation at the insertion position 95A). Thus, therewould be a total of 12.7×10⁶ unique members in the overall VK1-39library, as obtained by summing the number of unique members for each ofthe specified lengths. In certain embodiments of the invention, it maybe preferable to create the individual sub-libraries of lengths 8, 9 and10 separately, and then mix the sub-libraries in proportions thatreflect the length distribution of VKCDR3 in human sequences; forexample, in ratios approximating the 1:9:2 distribution that occurs innatural VKCDR3 sequences (see FIG. 3). The present invention providesthe compositions and methods for one of ordinary skill synthesizingVKCDR3 libraries corresponding to other VK chassis.

Example 7 A Minimalist Vλ CDR3 Library

This example describes the design of a minimalist VλCDR3 library. Theprinciples used in designing this library (or more complex Vλ libraries)are similar to those used to design the VKCDR3 libraries. However,unlike the VK genes, the contribution of the IgλV segment to CDRL3 isnot constrained to a fixed number of amino acids. Therefore, lengthvariation may be obtained in a minimalist VλCDR3 library even when onlyconsidering combinations between Vλ chassis and Jλ sequences.

Examination of the Vλ CDR3 lengths of human sequences shows that lengthsof 9 to 12 account for almost about 95% of sequences, and lengths of 8to 12 account for about 97% of sequences (FIG. 4). Table 36 shows theusage (percent occurrence) of the six known IGλJ genes in the rearrangedhuman lambda light chain sequences compiled from the NCBI database (seeAppendix B), and Table 37 shows the sequences encoded by the genes.

TABLE 36 IGλJ Gene Usage in the Lambda Light Chain Sequences Compiledfrom the NCBI Database (see Appendix B) Gene_Allele LUA Jλ1_01 20.2%Jλ2_01 42.2% Jλ3_02 36.2% Jλ6_01 0.6% Jλ7_01 0.9%

TABLE 37 Observed Human IGλJ Amino Acid Sequences Gene SequenceSEQ ID NO: IGλJ1-01 YVFGTGTKVTVL 557 IGλJ2-01 VVFGGGTKLTVL 558 IGλJ3-01WVFGGGTKLTVL 559 IGλJ3-02 VVFGGGTKLTVL 560 IGλJ6-01 NVFGSGTKVTVL 561IGλJ7-01 AVFGGGTQLTVL 562 IGλJ7-02 AVFGGGTQLTAL 563

IGλJ3-01 and IGλJ7-02 are not represented among the sequences that wereanalyzed; therefore, they were not included in Table 36. As illustratedin Table 36, IGλJ1-01, IGλJ2-01, and IGλJ3-02 are over-represented intheir usage, and have thus been bolded in Table 37. In some embodimentsof the invention, for example, only these three over-representedsequences may be utilized. In other embodiments of the invention, onemay use all six segments, any 1, 2, 3, 4, or 5 of the 6 segments, or anycombination thereof may be utilized.

As shown in Table 14, the portion of CDRL3 contributed by the IGλV genesegment is 7, 8, or 9 amino acids. The remainder of CDRL3 and FRM4 arederived from the IGλJ sequences (Table 37). The IGλJ sequencescontribute either one or two amino acids to CDRL3. If two amino acidsare contributed by IGλJ, the contribution is from the N-terminal tworesidues of the IGλJ segment: YV (IGλJ1-01), VV (IGλJ2-01), WV(IGλJ3-01), VV (IGλJ3-02), or AV (IGλJ7-01 and IGλJ7-02). If one aminoacid is contributed from IGλJ, it is a V residue, which is formed afterthe deletion of the N-terminal residue of a IGλJ segment.

In this non-limiting exemplary embodiment of the invention, the FRM4segment was fixed as FGGGTKLTVL, corresponding to IGλJ2-01 and IGλJ3-02(i.e., portions of SEQ ID NOs: 558 and 560).

Seven of the 11 selected chassis (W1-40 (SEQ ID NO: 531), W3-19 (SEQ IDNO: 536), W3-21 (SEQ ID NO: 537), W6-57 (SEQ ID NO: 539), W1-44 (SEQ IDNO: 532), W1-51 (SEQ ID NO: 533), and VλA-69 (SEQ ID NO: 538)) have anadditional two nucleotides following the last full codon. In four ofthose seven cases, analysis of the data set provided in Appendix Bshowed that the addition of a single nucleotide (i.e. without beinglimited by theory, via the activity of TdT) lead to a further increasein CDRL3 length. This effect can be considered by introducing variantsfor the L3-Vλ sequences contributed by these four ION sequences (Table38).

TABLE 38 Variants with an additional residue in CDRL3 CDR3/ SEQ NameLocus FRM1 CDR1 FRM2 CDR2 FRM3 L3-Vλ ID NO: 1E+ IGVλ1- QSVLTQPP TGSSSNIWYQQLPG YGN--- GVPDRFSGSKSG QSYDSS 564 40+ SVSGAPGQ GAGYD-- TAPKLLI-SNRPS --TSASLAITGL LSG S RVTISC -VH QAEDEADYYC 3L+ IGVλ3- SSELTQDPQGDSLRS WYQQKPG YGK--- GIPDRFSGSSSG NSRDSS 565 19+ AVSVALGQ -YY----QAPVLVI -NNRPS --NTASLTITGA GNH H/Q TVRITC -AS QAEDEADYYC 3H+ IGVλ3-SYVLTQPP GGNNIGS WYQQKPG YYD--- GIPERFSGSNSG QVWDSS 566 21+ SVSVAPGKKS----- QAPVLVI -SDRPS --NTATLTISRV SDH P TARITC -VH EAGDEADYYC 6A+IGVλ6_ NFMLTQPH TRSSGSI WYQQRPG YED--- GVPDRFSGSIDS QSYDSS 567 57+SVSESPGK ASNY--- SSPTTVI -NQRPS SSNSASLTISGL N H/Q -- TVTISC -VQKTEDEADYYC (+)sequences are derived from their parents by the additionof an amino acid at the end of the respective CDR3 (bold underlined).H/Q can be introduced in a single sequence by use of the degeneratecodon CAW or similar.Thus, the final set of chassis in the currently exemplified embodimentof the invention is 15: eleven contributed by the chassis in Table 14and an additional four contributed by the chassis of Table 38. Thecorresponding L3-Vλ domains of the 15 chassis contribute from 7 to 10amino acids to CDRL3. When considering the amino acids contributed bythe IGλJ sequences, the total variation in the length of CDRL3 is 8 to12 amino acids, approximating the distribution in FIG. 4. Thus, in thisexemplary embodiment of the invention, the minimalist Vλ library may berepresented by the following: 15 Chassis×5 IGλJ-derived segments=75sequences. Here, the 15 chassis are Vλ1-40 (SEQ ID NO: 531), Vλ1-44 (SEQID NO: 532), Vλ1-51 (SEQ ID NO: 533), Vλ2-14 (SEQ ID NO: 534), Vλ3-1*(SEQ ID NO: 535), Vλ3-19 (SEQ ID NO: 536), Vλ3-21 (SEQ ID NO: 537),Vλ4-69 (SEQ ID NO: 538), Vλ6-57 (SEQ ID NO: 539), Vλ5-45 (SEQ ID NO:540), Vλ7-43 (SEQ ID NO: 541), Vλ1-40+ (SEQ ID NO: 564), Vλ3-19+ (SEQ IDNO: 565), Vλ3-21+ (SEQ ID NO: 566), and Vλ6-57+ (SEQ ID NO: 567). The 5IGλJ-derived segments are YVFGGGTKLTVL (10 J1; SEQ ID NO: 568),VVFGGGTKLTVL (IGλJ2; SEQ ID NO: 558), WVFGGGTKLTVL (10 J3; SEQ ID NO:559), AVFGGGTKLTVL (10 J7; SEQ ID NO: 569), and -VFGGGTKLTVL (from anyof the preceding sequences).

Example 8 Matching to “Reference” Antibodies

CDRH3 sequences of human antibodies of interest that are known in theart, (e.g., antibodies that have been used in the clinic) have closecounterparts in the designed library of the invention. A set of fifteenCDRH3 sequences from clinically relevant antibodies is presented inTable 39.

TABLE 39 CDRH3 Sequences of Reference Antibodies Anti- SEQ body CDHR3 IDName Target Origin Status sequence NO: CAB1 TNF-α Phage FDA AKVSYLST 380display- Ap- ASSLDY human proved library CAB2 EGFR Transgenic  FDAVRDRVTGA 381 mouse Ap- FDI proved CAB3 IL-12/IL-23 Phage Phase KTHGSHDN382 display- III human library CAB4 Interleukin-  Transgenic PhaseARDLRTGP 383 1-β mouse III FDY CAB5 RANKL Transgenic Phase AKDPGTTV 384mouse III IMSWFDP CAB6 IL-12/IL-23 Transgenic Phase ARRRPGQG 385 mouseIII YFDF CAB7 TNF-α Transgenic Phase ARDRGASA 386 mouse III GGNYYYYG MDVCAB8 CTLA4 Transgenic Phase ARDPRGAT 387 mouse III LYYYYYGM DV CAB9 CD20Transgenic Phase AKDIQYGN 388 mouse III YYYGMDV CAB10 CD4 TransgenicPhase ARVINWFD 389 mouse III P CAB11 CTLA4 Transgenic Phase ARTGWLGP 390mouse III FDY CAB12 IGF1-R Transgenic Phase AKDLGWSD 391 mouse IISYYYYYGM DV CAB13 EGFR Transgenic Phase ARDGITMV 392 mouse II RGVMKDYFDY CAB14 EGFR Phage Phase ARVSIFGV 393 display- II GTFDY human libraryCAB15 BLyS Phage Phase ARSRDLLL 394 display- II FPHHALSP human library

Each of the above sequences was compared to each of the members of thelibrary of Example 5, and the member, or members, with the same lengthand fewest number of amino acid mismatches was, or were, recorded. Theresults are summarized in Table 40, below. For most of the cases,matches with 80% identity or better were found in the exemplified CDRH3library. To the extent that the specificity and binding affinity of eachof these antibodies is influenced by their CDRH3 sequence, without beingbound by theory, one or more of these library members could havemeasurable affinity to the relevant targets.

TABLE 40 Match of Reference Antibody CDRH3 to Designed Library %Identity Antibody Number of of Best Name Mismatches (*) Length MatchCAB1 5 14 64% CAB2 2 11 82% CAB3 4 8 50% CAB4 2 11 82% CAB5 3 15 80%CABG 3 12 75% CAB7 2 20 90% CAB8 0 19 100% CAB9 3 15 80% CAB10 1 9 89%CAB11 1 11 91% CAB12 2 18 89% CAB13 2 18 89% CAB14 1 13 92% CAB15 7 1656% (*) For the best-matching sequence(s) in library

Given that a physical realization of a library with about 10⁸ distinctmembers could, in practice, contain every single member, then suchsequences with close percent identity to antibodies of interest would bepresent in the physical realization of the library. This example alsohighlights one of many distinctions of the libraries of the currentinvention over those of the art; namely, that the members of thelibraries of the invention may be precisely enumerated. In contrast,CDRH3 libraries known in the art cannot be explicitly enumerated in themanner described herein. For example, many libraries known in the art(e.g., Hoet et al., Nat. Biotechnol., 2005, 23: 344; Griffiths et al.,EMBO J., 1994, 13: 3245; Griffiths et al., EMBO J., 1993, 12: 725; Markset al., J. Mol. Biol., 1991, 222: 581, each incorporated by reference inits entirety) are derived by cloning of natural human CDRH3 sequencesand their exact composition is not characterized, which precludesenumeration.

Synthetic libraries produced by other (e.g., random orsemi-random/biased) methods (Knappik, et al., J Mol Biol, 2000, 296: 57,incorporated by reference in its entirety) tend to have very largenumbers of unique members. Thus, while matches to a given input sequence(for example, at 80% or greater) may exist in a theoreticalrepresentation of such libraries, the probability of synthesizing andthen producing a physical realization of the theoretical library thatcontains such a sequence and then selecting an antibody corresponding tosuch a match, in practice, may be remotely small. For example, a CDRH3of length 19 in the Knappik library may have over 10¹⁹ distinctsequences. In a practical realization of such a library a tenth or so ofthe sequences may have length 19 and the largest total library may havein the order of 10¹⁰ to 10¹² transformants; thus, the probability of agiven pre-defined member being present, in practice, is effectively zero(less than one in ten million). Other libraries (e.g., Enzelberger etal. WO2008053275 and Ladner US20060257937, each incorporated byreference in its entirety) suffer from at least one of the limitationsdescribed throughout this application.

Thus, for example, considering antibody CAB14, there are seven membersof the designed library of Example 5 that differ at just one amino acidposition from the sequence of the CDRH3 of CAB14 (given in Table 39).Since the total length of this CDRH3 sequence is 13, the percent ofidentical amino acids is 12/13 or about 92% for each of these 7sequences of the library of the invention. It can be estimated that theprobability of obtaining such a match (or better) in the library ofKnappik et al. is about 1.4×10⁻⁹; it would be lower still, about5.5×10⁻¹⁰, in a library with equal amino acid proportions (i.e.,completely random). Therefore, in a physical realization of the librarywith about 10¹⁰ transformants of which about a tenth may have length 13,there may be one or two instances of these best matches. However, withlonger sequences such as CAB 12, the probability of having members inthe Knappik library with about 89% or better matching are under about10⁻¹⁵, so that the expected number of instances in a physicalrealization of the library is essentially zero. To the extent thatsequences of interest resemble actual human CDRH3 sequences, there willbe close matches in the library of Example 5, which was designed tomimic human sequences. Thus, one of the many relative advantages of thepresent library, versus those in the art, becomes more apparent as thelength of the CDRH3 increases.

Example 9 Split Pool Synthesis of Oligonucleotides Encoding the DH, N2,and H3-JH Segments

This example outlines the procedures used to synthesize theoligonucleotides used to construct the exemplary libraries of theinvention. Custom Primer Support™ 200 dT40S resin (GE Healthcare) wasused to synthesize the oligonucleotides, using a loading of about 39μmol/g of resin. Columns (diameter=30 μm) and frits were purchased fromBiosearch Technologies, Inc. A column bed volume of 30 μL was used inthe synthesis, with 120 nmol of resin loaded in each column. A mixtureof dichloromethane (DCM) and methanol (MeOH), at a ratio of 400/122(v/v) was used to load the resin. Oligonucleotides were synthesizedusing a Dr. Oligo® 192 oligonucleotide synthesizer and standardphosphorothioate chemistry.

The split pool procedure for the synthesis of the[DH]-[N2]-[H3-JH]oligonucleotides was performed as follows: First,oligonucleotide leader sequences, containing a randomly chosen 10nucleotide sequence (ATGCACAGTT; SEQ ID NO: 395), a BsrDI recognitionsite (GCAATG), and a two base “overlap sequence” (TG, AC, AG, CT, or GA)were synthesized. The purpose of each of these segments is explainedbelow. After synthesis of this 18 nucleotide sequence, the DH segmentswere synthesized; approximately 1 g of resin (with the 18 nucleotidesegment still conjugated) was suspended in 20 mL of DCM/MeOH. About 60μL of the resulting slurry (120 nmol) was distributed inside each of 278oligonucleotide synthesis columns. These 278 columns were used tosynthesize the 278 DH segments of Table 18, 3′ to the 18 nucleotidesegment described above. After synthesis, the 278 DH segments werepooled as follows: the resin and frits were pushed out of the columnsand collected inside a 20 mL syringe barrel (without plunger). Eachcolumn was then washed with 0.5 mL MeOH, to remove any residual resinthat was adsorbed to the walls of the column. The resin in the syringebarrel was washed three times with MeOH, using a low porosity glassfilter to retain the resin. The resin was then dried and weighed.

The pooled resin (about 1.36 g) containing the 278 DH segments wassubsequently suspended in about 17 mL of DCM/MeOH, and about 60 μL ofthe resulting slurry was distributed inside each of two sets of 141columns. The 141 N2 segments enumerated in Tables 24 and 25 were thensynthesized, in duplicate (282 total columns), 3′ to the 278 DH segmentssynthesized in the first step. The resin from the 282 columns was thenpooled, washed, and dried, as described above.

The pooled resin obtained from the N2 synthesis (about 1.35 g) wassuspended in about 17 mL of DCM/MeOH, and about 60 μL of the resultingslurry was distributed inside each of 280 columns, representing 28 H3-JHsegments synthesized ten times each. A portion (described more fullybelow) of each of the 28 IGHJ segments, including H3-JH of Table 20 werethen synthesized, 3′ to the N2 segments, in ten of the columns. Finaloligonucleotides were cleaved and deprotected by exposure to gaseousammonia (85° C., 2 h, 60 psi).

Split pool synthesis was used to synthesize the exemplary CDRH3 library.However, it is appreciated that recent advances in oligonucleotidesynthesis, which enable the synthesis of longer oligonucleotides athigher fidelity and the production of the oligonucleotides of thelibrary by synthetic procedures that involve splitting, but not pooling,may be used in alternative embodiments of the invention. The split poolsynthesis described herein is, therefore, one possible means ofobtaining the oligonucleotides of the library, but is not limiting. Oneother possible means of synthesizing the oligonucleotides described inthis application is the use of trinucleotides. This may be expected toincrease the fidelity of the synthesis, since frame shift mutants wouldbe reduced or eliminated.

Example 10 Construction of the CDRH3 and Heavy Chain Libraries

This example outlines the procedures used to create exemplary CDRH3 andheavy chain libraries of the invention. A two step process was used tocreate the CDRH3 library. The first step involved the assembly of a setof vectors encoding the tail and N1 segments, and the second stepinvolved utilizing the split pool nucleic acid synthesis proceduresoutlined in Example 9 to create oligonucleotides encoding the DH, N2,and H3-JH segments. The chemically synthesized oligonucleotides werethen ligated into the vectors, to yield CDRH3 residues 95-102, based onthe numbering system described herein. This CDRH3 library wassubsequently amplified by PCR and recombined into a plurality of vectorscontaining the heavy chain chassis variants described in Examples 1 and2. CDRH1 and CDRH2 variants were produced by QuikChange® Mutagenesis(Stratagene™), using the oligonucleotides encoding the ten heavy chainchassis of Example 1 as a template. In addition to the heavy chainchassis, the plurality of vectors contained the heavy chain constantregions (i.e., CH1, CH2, and CH3) from IgG1, so that a full-length heavychain was formed upon recombination of the CDRH3 with the vectorcontaining the heavy chain chassis and constant regions. In thisexemplary embodiment, the recombination to produce the full-length heavychains and the expression of the full-length heavy chains were bothperformed in S. cerevisiae.

To generate full-length, heterodimeric IgGs, comprising a heavy chainand a light chain, a light chain protein was also expressed in the yeastcell. The light chain library used in this embodiment was the kappalight chain library, wherein the VKCDR3s were synthesized usingdegenerate oligonucleotides (see Example 6.2). Due to the shorter lengthof the oligonucleotides encoding the light chain library (in comparisonto those encoding the heavy chain library), the light chain CDR3oligonucleotides could be synthesized de novo, using standard proceduresfor oligonucleotide synthesis, without the need for assembly fromsub-components (as in the heavy chain CDR3 synthesis). One or more lightchains can be expressed in each yeast cell which expresses a particularheavy chain clone from a library of the invention. One or more lightchains have been successfully expressed from both episomal (e.g.,plasmid) vectors and from integrated sites in the yeast genome.

Below are provided further details on the assembly of the individualcomponents for the synthesis of a CDRH3 library of the invention, andthe subsequent combination of the exemplary CDRH3 library with thevectors containing the chassis and constant regions. In this particularexemplary embodiment of the invention, the steps involved in the processmay be generally characterized as (i) synthesis of 424 vectors encodingthe tail and N1 regions; (ii) ligation of oligonucleotides encoding the[DH]-[N2]-[H3-JH] segments into these 424 vectors; (iii) PCRamplification of the CDRH3 sequences from the vectors produced in theseligations; and (iv) homologous recombination of these PCR-amplifiedCDRH3 domains into the yeast expression vectors containing the chassisand constant regions.

Example 10.1 Synthesis of Vectors Encoding the Tail and N1 Regions

This example demonstrates the synthesis of 424 vectors encoding the tailand N1 regions of CDRH3. In this exemplary embodiment of the invention,the tail was restricted to G, D, E, or nothing, and the N1 region wasrestricted to one of the 59 sequences shown in Table 24. As describedthroughout the specification, many other embodiments are possible.

In the first step of the process, a single “base vector” (pJM204, apUC-derived cloning vector) was constructed, which contained (i) anucleic acid sequence encoding two amino acids that are common to theC-terminal portion of all 28 IGHJ segments (SS), and (ii) a nucleic acidsequence encoding a portion of the CH1 constant region from IgG1. Thus,the base vector contains an insert encoding a sequence that can bedepicted as:

[SS]-[CH1˜],

wherein SS is a common portion of the C-terminus of the 28 IGHJ segmentsand CH1˜ is a portion of the CH1 constant region from IgG1, namely:

(SEQ ID NO: 396) ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLG.

Next, 424 different oligonucleotides were cloned into the base vector,upstream (i.e., 5′) from the region encoding the [SS]-[CH1˜]. These 424oligonucleotides were synthesized by standard methods and each encoded aC-terminal portion of one of the 17 heavy chain chassis enumerated inTable 5, plus one of four exemplary tail segments (G/D/E/-), and one of59 exemplary N1 segments (Table 24). These 424 oligonucleotides,therefore, encode a plurality of sequences that may be represented by:

[˜FRM3]-[G/D/E/-]-[N1],

wherein ˜FRM3 represents a C-terminal portion of a FRM3 region from oneof the 17 heavy chain chassis of Table 5, G/D/E/- represents G, D, E, ornothing, and N1 represents one of the 59 N1 sequences enumerated inTable 24. As described throughout the specification, the invention isnot limited to the chassis exemplified in Table 5, their CDRH1 and CDRH2variants (Table 8), the four exemplary tail options used in thisexample, or the 59 N1 segments presented in Table 24.

The oligonucleotide sequences represented by the sequences above weresynthesized in two groups: one group containing a FRM3 region identicalto the corresponding region on 16 of the 17 the heavy chain chassisenumerated in Table 5, and another group containing a FRM3 region thatis identical to the corresponding region on VH3-15. In the former group,an oligonucleotide encoding DTAVYYCAR (SEQ ID NO: 397) was used forFRM3. During subsequent PCR amplification, the V residue of VH5-51 wasaltered to an M, to correspond to the VH5-51 germline sequence. In thelatter group (that with a sequence common to VH3-15), a largeroligonucleotide, encoding the sequenceAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK (SEQ ID NO: 398) wasused for ˜FRM3. Each of the two oligonucleotides encoding the ˜FRM3regions were paired with oligonucleotides encoding one of the four tailregions (G/D/E/-) and one of the 59 N1 segments, yielding a total of 236possible combinations for each ˜FRM3 (i.e., 1×4×59), or a total of 472possible combinations when both ˜FRM3 sequences are considered. However,48 of these combinations are redundant and only a single representationof these sequences was used in the currently exemplified CDRH3 library,yielding 424 unique oligonucleotides encoding [˜FRM3]-[G/D/E/-]-[N1]sequences.

After the oligonucleotides encoding the [˜FRM3]-[G/D/E/-]-[N1] and[SS]-[CH1˜] segments were cloned into the vector, as described above,additional sequences were added to the vector to facilitate thesubsequent insertion of the oligonucleotides encoding the[DH]-[N2]-[H3-JH] fragments synthesized during the split pool synthesis.These additional sequences comprise a polynucleotide encoding aselectable marker protein, flanked on each side by a recognition sitefor a type II restriction enzyme, for example:

[Type II RS 1]-[selectable marker protein]-[Type II RS 2].

In this exemplary embodiment, the selectable marker protein is ccdB andthe type II restriction enzyme recognition sites are specific for BsrDIand BbsI. In certain strains of E. coli, the ccdB protein is toxic,thereby preventing the growth of these bacteria when the gene ispresent.

An example of the 5′ end of one of the 212 vectors with a ˜FRM3 regionbased on the VH3-23 chassis, D tail residue and an N1 segment of lengthzero is presented below (SEQ ID NO: 570):

An example of one of the 212 vectors with a ˜FRM3 region based on one ofthe other 16 chassis, with a D residue as the tail and an N1 segment oflength zero is presented below (SEQ ID NO: 571):

All 424 vectors were sequence verified. A schematic diagram of thecontent of the 424 vectors, before and after cloning of the[DH]-[N2]-[H3-JH] fragment is presented in FIG. 5. Below is an exemplarysequence from one of the 424 vectors containing a FRM3 region fromVH3-23 (SEQ ID NO: 572).

Example 10.2 Cloning of the Oligonucleotides Encoding the DH, N2, H3-JHSegments into the Vectors Containing the Tail and N1 Segments

This example describes the cloning of the oligonucleotides encoding the[D]-[N2]-[H3-JH] segments (made via split pool synthesis; Example 9)into the 424 vectors produced in Example 10.1. To summarize, the[DH]-[N2]-[H3-JH] oligonucleotides produced via split pool synthesiswere amplified by PCR, to produce double-stranded oligonucleotides, tointroduce restriction sites that would create overhangs complementary tothose on the vectors (i.e., BsrDI and BbsI), and to complete the 3′portion of the IGHJ segments that was not synthesized in the split poolsynthesis. The amplified oligonucleotides were then digested with therestriction enzymes BsrDI (cleaves adjacent to the DH segment) and BbsI(cleaves near the end of the JH segment). The cleaved oligonucleotideswere then purified and ligated into the 424 vectors which had previouslybeen digested with BsrDI and BbsI. After ligation, the reactions werepurified, ethanol precipitated, and resolubilized.

This process for one of the [DH]-[N2]-[H3-JH] oligonucleotidessynthesized in the split pool synthesis is illustrated below. Thefollowing oligonucleotide (SEQ ID NO: 399) is one of theoligonucleotides synthesized during the split pool synthesis:

 1 ATGCACAGTTGCAATG TG TATTACTATGGATCTGGTTCTTA 50 CTATAAT GT 51 GGGCGGATATTATTACTACTATGGTATGGACGTATGGGGGC 99 AAGGGACC

The first 10 nucleotides (ATGCACAGTT; SEQ ID NO: 395) represent aportion of a random sequence that is increased to 20 base pairs in thePCR amplification step, below. This portion of the sequence increasesthe efficiency of BsrDI digestion and facilitates the downstreampurification of the oligonucleotides.

Nucleotides 11-16 (underlined) represent the BsrDI recognition site. Thetwo base overlap sequence that follows this site (in this example TG;bold) was synthesized to be complementary to the two base overhangcreated by digesting certain of the 424 vectors with BsrDI (i.e.,depending on the composition of the tail/N1 region of the particularvector). Other oligonucleotides contain different two-base overhangs, asdescribed below.

The two base overlap is followed by the DH gene segment (nucleotides19-48), in this example, by a 30 bp sequence(TATTACTATGGATCTGGTTCTTACTATAAT, SEQ ID NO: 400) which encodes the tenresidue DH segment YYYGSGSYYN (i.e., IGHD3-10_(—)2 of Table 17; SEQ IDNO: 2).

The region of the oligonucleotide encoding the DH segment is followed,in this example, by a nine base region (GTGGGCGGA; bold; nucleotides49-57), encoding the N2 segment (in this case VGG; Table 24).

The remainder of this exemplary oligonucleotide represents the portionof the JH segment that is synthesized during the split pool synthesis(TATTATTACTACTATGGTATGGACGTATGGGGGCAAGGGACC; SEQ ID NO: 401; nucleotides58-99; underlined), encoding the sequence YYYYYGMDVWGQGT (Table 20;residues 1-14 of SEQ ID NO: 258). The balance of the IGHJ segment isadded during the subsequent PCR amplification described below.

After the split pool-synthesized oligonucleotides were cleaved from theresin and deprotected, they served as a template for a PCR reactionwhich added an additional randomly chosen 10 nucleotides (e.g.,GACGAGCTTC; SEQ ID NO: 402) to the 5′ end and the rest of the IGHJsegment plus the BbsI restriction site to the 3′ end. These additionsfacilitate the cloning of the [DH]-[N2]-[JH] oligonucleotides into the424 vectors. As described above (Example 9), the last round of the splitpool synthesis involves 280 columns: 10 columns for each of theoligonucleotides encoding one of 28 H3-JH segments. The oligonucleotideproducts obtained from these 280 columns are pooled according to theidentity of their H3-JH segments, for a total of 28 pools. Each of these28 pools is then amplified in five separate PCR reactions, using fiveforward primers that each encode a different two base overlap (precedingthe DH segment; see above) and one reverse primer that has a sequencecorresponding to the familial origin of the H3-JH segment beingamplified. The sequences of these 11 primers are provided below:

Forward primers AC (SEQ ID NO: 403) GACGAGCTTCAATGCACAGTTGCAATGAC  AG(SEQ ID NO: 404) GACGAGCTTCAATGCACAGTTGCAATGAG  CT (SEQ ID NO: 405)GACGAGCTTCAATGCACAGTTGCAATGCT  GA (SEQ ID NO: 406)GACGAGCTTCAATGCACAGTTGCAATGGA  TG (SEQ ID NO: 407)GACGAGCTTCAATGCACAGTTGCAATGTG  Reverse Primers JH1  (SEQ ID NO: 408)TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACGGTGACCAAGG TGCCCTGGCCCCA JH2 (SEQ ID NO: 409) TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACAGTGACCAAGGTGCCACGGCCCCA JH3 (SEQ ID NO: 410)TGCATCAGTGCGACTAACGGAAGACTCTGAAGAGACGGTGACCATTG TCCCTTGGCCCCA JH4(SEQ ID NO: 411) TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACGGTGACCAAGGTTCCTTGGCCCCA JH5 (SEQ ID NO: 412)TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACGGTGACCAAGG TTCCCTGGCCCCA JH6(SEQ ID NO: 413) TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACGGTGACCGTGGTCCCTTGCCCCCA

Amplifications were performed using Taq polymerase, under standardconditions. The oligonucleotides were amplified for eight cycles, tomaintain the representation of sequences of different lengths. Meltingof the strands was performed at 95° C. for 30 seconds, with annealing at58° C. and a 15 second extension time at 72° C.

Using the exemplary split-pool derived oligonucleotide enumerated aboveas an example, the PCR amplification was performed using the TG primerand the JH6 primer, where the annealing portion of the primers has beenunderlined:

TG (SEQ ID NO: 407) GACGAGCTTCAATGCACAGTTGCAATGTG JH6 (SEQ ID NO: 413)TGCATCAGTGCGACTAACGGAAGACTCTGAGGAGACGGTGACCGTGG TCCCTTGCCCCCAThe portion of the TG primer that is 5′ to the annealing portionincludes the random 10 base pairs described above. The portion of theJH6 primer that is 5′ to the annealing portion includes the balance ofthe JH6 segment and the BbsI restriction site. The following PCR product(SEQ ID NO: 414) is formed in the reaction (added sequences underlined):

GACGAGCTTCATGCACAGTTGCAATGTGTATTACTATGGATCTGGTTCTTACTATAATGTGGGCGGATATTATTACTACTATGGTATGGACGTATGGGGGCAAGGGACCACGGTCACCGTCTCCTCAGAGTCTTCCGTTAG TCGCACTGATGCAG

The PCR products from each reaction were then combined into five pools,based on the forward primer that was used in the reaction, creating setsof sequences yielding the same two-base overhang after BsrDI digestion.The five pools of PCR products were then digested with BsRDI and BbsI(100 μg of PCR product; 1 mL reaction volume; 200 U BbsI; 100 U BsrDI; 2h; 37° C.; NEB Buffer 2). The digested oligonucleotides were extractedtwice with phenol/chloroform, ethanol precipitated, air dried brieflyand resolubilized in 300 μL of TE buffer by sitting overnight at 4° C.

Each of the 424 vectors described in the preceding sections was thendigested with BsrDI and BbsI, each vector yielding a two base overhangthat was complimentary to one of those contained in one of the fivepools of PCR products. Thus, one of the five pools of restrictiondigested PCR products are ligated into each of the 424 vectors,depending on their compatible ends, for a total of 424 ligations.

Example 10.3 PCR Amplification of the CDRH3 from the 424 Vectors

This example describes the PCR amplification of the CDRH3 regions fromthe 424 vectors described above. As set forth above, the 424 vectorsrepresent two sets: one for the VH3-23 family, with FRM3 ending in CAK(212 vectors) and one for the other 16 chassis, with FRM3 ending in CAR(212 vectors). The CDRH3s in the VH3-23-based vectors were amplifiedusing a reverse primer (EK137; see Table 41) recognizing a portion ofthe CH1 region of the plasmid and the VH3-23-specific primer EK135 (seeTable 41). Amplification of the CDRH3s from the 212 vectors with FRM3ending in CAR was performed using the same reverse primer (EK137) andeach of five FRM3-specific primers shown in Table 41 (EK139, EK140,EK141, EK143, and EK144). Therefore, 212 VH3-23 amplifications and 212×5FRM3 PCR reactions were performed, for a total of 1,272 reactions. Anadditional PCR reaction amplified the CDRH3 from the 212 VH3-23-basedvectors, using the EK 133 forward primer, to allow the amplicons to becloned into the other 5 VH3 family member chassis while making the lastthree amino acids of these chassis CAK instead of the original CAR(VH3-23*). The primers used in each reaction are shown in Table 41.

TABLE 41 Primers Used for Amplification of CDRH3 Sequences SEQ PrimerCompatible ID No. Chassis Primer Sequence NO EK135 VH3-23CACATACTACGCAGACTCCGTG 415 EK133 VH3-48; CAAATGAACAGCCTGAGAGCCG 416VH3-7; AGGACACGGCGGTGTACTACTG VH3-15; VH3-30; VH3-33; VH3-23* EK139VH4-B; AAGCTGAGTTCTGTGACCGCCG 417 VH4-31; CAGACACGGCGGTGTACTACTG VH4-34;VH4-39; VH4-59; VH4-61 EK140 VH1-46; GAGCTGAGCAGCCTGAGATCTG 418 VH1-69AGGACACGGCGGTGTACTACTG EK141 VH1-2 GAGCTGAGCAGGCTGAGATCTG 419ACGACACGGCGGTGTACTACTG EK143 VH5-51 CAGTGGAGCAGCCTGAAGGCCT 420CGGACACGGCGATGTACTACTG EK144 VH1-18 GAGCTGAGGAGCCTGAGATCTG 421ACGACACGGCGGTGTACTACTG EK137 CH1 Rev. GTAGGACAGCCGGGAAGG 422 Primer

Example 10.4 Homologous Recombination of PCR Amplified CDRH3 Regionsinto Heavy Chain Chassis

After amplification, reaction products were pooled according to therespective VH chassis that they would ultimately be cloned into. Table42 enumerates these pools, with the PCR primers used to obtain the CDRH3sequences in each pool provided in the last two columns.

TABLE 42 PCR Primers Used to Amplify CDRH3 Regions from 424 Vectors Pool# (Arbitrary) HC Chassis Target 5′ Primer 3′ Primer 1 1-46 EK140 EK1371-69 EK140 EK137 2 1-2 EK141 EK137 3 1-18 EK144 EK137 4 4-B EK139 EK1374-31 EK139 EK137 4-34² EK139 EK137 4-39 EK139 EK137 4-59 EK139 EK1374-61 EK139 EK137 5 5-51 EK143 EK137 6 3-15¹ EK133 EK137 3-7 EK133 EK1373-33 EK133 EK137 3-33 EK133 EK137 3-48 EK133 EK137 7 3-23 EMK135 EK137 83-23* EK133 EK137 *Allowed the amplicons to be cloned into the other 5VH3 family member chassis (i.e., other than VH3-23), while making thelast three amino acids of these chassis CAK instead of the original CAR.¹As described in Table 5, the original KT sequence in VH3-15 was mutatedto RA, and the original TT to AR. ²As described in Table 5, thepotential site for N-linked glycosylation was removed from CDRH2 of thischassis.

After pooling of the amplified CDRH3 regions, according to the processoutlined above, the heavy chain chassis expression vectors were pooledaccording to their origin and cut, to create a “gap” for homologousrecombination with the amplified CDRH3s. FIG. 6 shows a schematicstructure of a heavy chain vector, prior to recombination with a CDRH3.In this exemplary embodiment of the invention, there were a total of 152vectors encoding heavy chain chassis and IgG1 constant regions, but noCDRH3. These 152 vectors represent 17 individual variable heavy chaingene families (Table 5; Examples 1 and 2). Fifteen of the families wererepresented by the heavy chain chassis sequences described in Table 5and the CDRH1/H2 variants described in Table 8 (i.e., 150 vectors). VH3-30 differs from VH3-33 by a single amino acid; thus VH3-30 wasincluded in the VH3-33 pool of variants. The 4-34 VH family member waskept separate from all others and, in this exemplary embodiment, novariants of it were included in the library. Thus, a total of 16 pools,representing 17 heavy chain chassis, were generated from the 152vectors.

The vector pools were digested with the restriction enzyme SfiI, whichcuts at two sites in the vector that are located between the end of theFRM3 of the variable domain and the start of the CH1 (SEQ ID NO: 573).

The gapped vector pools were then mixed with the appropriate (i.e.,compatible) pool of CDRH3 amplicons, generated as described above, at a50:1 insert to vector ratio. The mixture was then transformed intoelectrocompetent yeast (S. cerevisiae), which already contained plasmidsor integrated genes comprising a VK light chain library (describedbelow). The degree of library diversity was determined by plating adilution of the electroporated cells on a selectable agar plate. In thisexemplified embodiment of the invention, the agar plate lackedtryptophan and the yeast lacked the ability to endogenously synthesizetryptophan. This deficiency was remedied by the inclusion of the TRPmarker on the heavy chain chassis plasmid, so that any yeast receivingthe plasmid and recombining it with a CDRH3 insert would grow. Theelectroporated cells were then outgrown approximately 100-fold, inliquid media lacking tryptophan. Aliquots of the library were frozen in50% glycerol and stored at −80° C. Each transformant obtained at thisstage represents a clone that can express a full IgG molecule. Aschematic diagram of a CDRH3 integrated into a heavy chain vector andthe accompanying sequence are provided in FIG. 5.

A heavy chain library pool was then produced, based on the approximaterepresentation of the heavy chain family members as depicted in Table43.

TABLE 43 Occurrence of Heavy Chain Chassis in Data Sets Used to DesignLibrary, Expected (Designed) Library, and Actual (Observed) LibraryRelative Occurrence in Chassis Data Sets (1) Expected (2) Observed (3)VH1-2 5.1 6.0 6.4 VH1-18 3.4 3.7 3.8 VH1-46 3.4 5.2 4.7 VH1-69 8.0 8.010.7 VH3-7 3.6 6.1 4.5 VH3-15 1.9 6.9 3.6 VH3-23 11.0 13.2 17.1VH3-33/30 13.1 12.5 6.6 VH3-48 2.9 6.3 7.5 VH4-31 3.4 2.5 4.3 VH4-3417.2 7.0 4.7 VH4-39 8.7 3.9 3.0 VH4-59 7.0 7.8 9.2 VH4-61 3.2 1.9 2.4VH4-B 1.0 1.4 0.8 VH5-51 7.2 7.7 10.5 (1) As detailed in Example 1,these 17 sequences account for about 76% of the entire sample of humanVH sequences used to represent the human repertoire. (2) Based onpooling of sub-libraries of each chassis type. (3) Usage in 531sequences from library; cf. FIG. 20.

Example 10.5 K94R Mutation in VH3-23 and R94K Mutation in VH3-33,VH3-30, VH3-7, and VH3-48

This example describes the mutation of position 94 in VH3-23, VH3-33,VH3-30, VH3-7, and VH3-48. In VH3-23, the amino acid at this positionwas mutated from K to R. In VH3-33, VH3-30, VH3-7, and VH3-48, thisamino acid was mutated from R to K. In VH3-32, this position was mutatedfrom K to R. The purpose of making these mutations was to enhance thediversity of CDRH3 presentation in the library. For example, innaturally occurring VH3-23 sequences, about 90% have K at position 94,while about 10% have position R. By making these changes the diversityof the CDRH3 presentation is increased, as is the overall diversity ofthe library.

Amplification was performed using the 424 vectors as a template. For theK94R mutation, the vectors containing the sequence DTAVYYCAK (VH3-23;SEQ ID NO: 578) were amplified with a PCR primer that changed the K to aR and added 5′ tail for homologous recombination with the VH3-48,VH3-33, VH-30, and VH3-7. The “T” base in 3-48 does not change the aminoacid encoded and thus the same primer with a T::C mismatch still allowshomologous recombination into the 3-48 chassis.

Furthermore, the amplification products from the 424 vectors (producedas described above) containing the DTAVYYCAR (SEQ ID NO: 579) sequencecan be homologously recombined into the VH3-23 (CAR) vector, changing Rto K in this framework and thus further increasing the diversity ofCDRH3 presentation in this chassis.

VH3-48 (240) SEQ ID NO: (574)240                                         TCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCGGTGTACT           294 ACTGCGCCAGAVH3-33/30 (240) SEQ ID NO: (575)TCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCGGTGTACT ACTGCGCCAGA VH3-7 (240)SEQ ID NO: (576) TCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCGGTGTACTACTGCGCCAGA VH3-23 (240) SEQ ID NO: (577)TCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCGGTGTACT ACTGCGCCAAG

Example 11 VK Library Construction

This example describes the construction of a VK library of theinvention. The exemplary VK library described herein corresponds to theVKCDR3 library of about 10⁵ complexity, described in Example 6.2. Asdescribed in Example 6, and throughout the application, other VKlibraries are within the scope of the invention, as are Vλ libraries.

Ten VK chassis were synthesized (Table 11), which did not containVKCDR3, but instead had two SfiI restriction sites in the place ofVKCDR3, as for the heavy chain vectors. The kappa constant regionfollowed the SfiI restriction sites. FIG. 8 shows a schematic structureof a light chain vector, prior to recombination with a CDRL3.

Ten VKCDR oligonucleotide libraries were then synthesized, as describedin Example 6.2, using degenerate oligonucleotides (Table 33). Theoligonucleotides were then PCR amplified, as separate pools, to makethem double stranded and to add additional nucleotides required forefficient homologous recombination with the gapped (by SfiI) vectorcontaining the VK chassis and constant region sequences. The VKCDR3pools in this embodiment of the invention represented lengths 8, 9, and10 amino acids, which were mixed post-PCR at a ratio 1:8:1. The poolswere then cloned into the respective SfiI gapped VK chassis viahomologous recombination, as described for the CDRH3 regions, set forthabove. A schematic diagram of a CDRL3 integrated into a light chainvector and the accompanying sequence are provided in FIG. 9.

A kappa light chain library pool was then produced, based on theapproximate representation of the VK family members found in thecirculating pool of B cells. The 10 kappa variable regions used and therelative frequency in the final library pool are shown in Table 44.

TABLE 44 Occurrence of VK Chassis in Data Sets Used to Design Library,Expected (Designed) Library, and Actual (Observed) Library RelativeOccurrence in Chassis Data Sets (1) Expected (2) Observed (3) VK1-5 8.67.1 5.8 VK1-12 4.0 3.6 3.5 VK1-27 3.3 3.6 8.1 VK1-33 5.3 7.1 3.5 VK1-3918.5 21.4 17.4 VK2-28 7.7 7.1 5.8 VK3-11 10.9 10.7 20.9 VK3-15 6.6 7.14.7 VK3-20 24.5 21.4 18.6 VK4-1 10.4 10.7 11.6 (1) As indicated inExample 3, these 10 chassis account for about 80% of the occurrences inthe entire data set of VK sequences examined. (2) Rounded off ratiosfrom the data in column 2, then normalized for actual experimental setup. The relative rounded ratios are 6 for VK1-39 and VK3-20, 3 forVK3-11 and VK4-1, 2 for VK-15, VK1-33, VK2-28 and VK3-15, and 1 forVK1-12 and VK1-27. (3) Chassis usage in set of 86 sequences obtainedfrom library; see also FIG. 22.

Example 12 Characterization of Exemplary Libraries

This example shows the characteristics of exemplary libraries of theinvention, constructed according to the methods described herein.

Example 12.1 Characterization of the Heavy Chains

To characterize the product of the split pool synthesis, ten of the 424vectors containing the [Tail]-[N1]-[DH]-[N2]-[H3-JH] product wereselected at random and transformed into E. coli. The split pool producthad a theoretical diversity of about 1.1×10⁶ (i.e., 278×141×28).Ninety-six colonies were selected from the transformation and forwardand reverse sequences were generated for each clone. Of the 96sequencing reactions, 90 yielded sequences from which the CDRH3 regioncould be identified, and about 70% of these sequences matched a designedsequence in the library. The length distribution of the sequenced CDRH3segments from the ten vectors, as compared to the theoreticaldistribution (based on design), is provided in FIG. 10. The lengthdistribution of the individual DH, N2, and H3-JH segments obtained fromthe ten vectors are shown in FIGS. 11-13.

Once the length distribution of the CDRH3 components of the library thatwere contained in the vector matched design were verified, the CDRH3domains and heavy chain family representation in yeast that had beentransformed according to the process described in Example 10.4 werecharacterized. Over 500 single-pass sequences were obtained. Of these,531 yielded enough sequence information to identify the heavy chainchassis and 291 yielded enough sequence information to characterize theCDRH3. These CDRH3 domains have been integrated with the heavy chainchassis and constant region, according to the homologous recombinationprocesses described herein. The length distribution of the CDRH3 domainsfrom 291 sequences, compared to the theoretical length distribution, isshown in FIG. 14. The mean theoretical length was 14.4±4 amino acids,while the average observed length was 14.3±3 amino acids. The observedlength of each portion of the CDRH3, as compared to theoretical, ispresented in FIGS. 15-18. FIG. 19 depicts the familial origin of the JHsegments identified in the 291 sequences, and FIG. 20 shows therepresentation of 16 of the chassis of the library. The VH3-15 chassiswas not represented amongst these sequences. This was corrected later byintroducing yeast transformants containing the VH3-15 chassis, withCDRH3 diversity, into the library at the desired composition.

Example 12.2 Characterization of the Light Chains

The length distribution of the CDRL3 components, from the VKCDR3 librarydescribed in Example 6.2, were determined after yeast transformation viathe methods described in Example 10.4. A comparison of the CDRL3 lengthfrom 86 sequences of the library to the human sequences and designedsequences is provided in FIG. 21. FIG. 22 shows the representation ofthe light chain chassis from amongst the 86 sequences selected from thelibrary. About 91% of the CDRL3 sequences were exact matches to thedesign, and about 9% differed by a single amino acid.

Example 13 Characterization of the Composition of the Designed CDRH3Libraries

This example presents data on the composition of the CDRH3 domains ofexemplary libraries, and a comparison to other libraries of the art.More specifically, this example presents an analysis of the occurrenceof the 400 possible amino acid pairs (20 amino acids×20 amino acids)occurring in the CDRH3 domains of the libraries. The prevalence of thesepairs is computed by examination of the nearest neighbor (i-i+1;designated IP1), next nearest neighbor (i-i+2; designated IP2), andnext-next nearest neighbor (i-i+3; designated IP3) of the i residue inCDRH3. Libraries previously known in the art (e.g., Knappik et al., J.Mol. Biol., 2000, 296: 57; Sidhu et al., J. Mol. Biol., 2004, 338: 299;and Lee et al., J. Mol. Biol. 2004, 340: 1073, each of which isincorporated by reference in its entirety) have only considered theoccurrence of the 20 amino acids at individual positions within CDRH3,while maintaining the same composition across the center of CDRH3, andnot the pair-wise occurrences considered herein. In fact, according toSidhu et al. (J. Mol. Biol., 2004, 338: 299, incorporated by referencein its entirety), “[i]n CDR-H3, there was some bias towards certainresidue types, but all 20 natural amino acid residues occurred to asignificant extent, and there was very little position-specific biaswithin the central portion of the loop”. Thus, the present inventionrepresents the first recognition that, surprisingly, a position-specificbias does exist within the central portion of the CDRH3 loop, when theoccurrences of amino acid pairs recited above are considered. Thisexample shows that the libraries described herein more faithfullyreproduce the occurrence of these pairs as found in human sequences, incomparison to other libraries of the art. The composition of thelibraries described herein may thus be considered more “human” thanother libraries of the art.

To examine the pair-wise composition of CDRH3 domains, a portion ofCDRH3 beginning at position 95 was chosen. For the purposes ofcomparison with data presented in Knappik et al. and Lee et al., thelast five residues in each of the analyzed CDRH3s were ignored. Thus,for the purposes of this analysis, both members of the pair i-i+X (X=1to 3) must fall within the region starting at position 95 and ending at(but including) the sixth residue from the C-terminus of the CDRH3. Theanalyzed portion is termed the “central loop” (see Definitions).

To estimate pair distributions in representative libraries of theinvention, a sampling approach was used. A number of sequences weregenerated by choosing randomly and, in turn, one of the 424 tail plus N1segments, one of the 278 DH segments, one of the 141 N2 segments and oneof the 28 JH segments (the latter truncated to include only the 95 to102 Kabat CDRH3). The process was repeated 10,000 times to generate asample of 10,000 sequences. By choosing a different seed for the randomnumber generation, an independent sample of another 10,000 sequences wasalso generated and the results for pair distributions were observed tobe nearly the same. For the calculations presented herein, a third andmuch larger sample of 50,000 sequences was used. A similar approach wasused for the alternative library embodiment (N-1-141), whereby the firstsegment was selected from 1068 tail+N1 segments (resulting aftereliminating redundant sequences from 2 times 4 times 141 or 1128possible combinations).

The pair-wise composition of Knappik et al. was determined based on thepercent occurrences presented in FIG. 7 a of Knappik et al. (p. 71). Therelevant data are reproduced below, in Table 45.

TABLE 45 Composition of CDRH3 positions 95-100s (corresponding topositions 95-99B of the libraries of the current invention) of CDRH3 ofKnappik et al. (from FIG. 7a of Knappik et al.) Amino Acid Planned (%)Found (%) A 4.1 3.0 C 1.0 1.0 D 4.1 4.2 E 4.1 2.3 F 4.1 4.9 G 15.0 10.8H 4.1 4.6 I 4.1 4.5 K 4.1 2.9 L 4.1 6.6 M 4.1 3.3 N 4.1 4.5 P 4.1 4.8 Q4.1 2.9 R 4.1 4.1 S 4.1 5.6 T 4.1 4.5 V 4.1 3.7 W 4.1 2.0 Y 15.0 19.8

The pair-wise composition of Lee et al. was determined based on thelibraries depicted in Table 5 of Lee et al., where the positionscorresponding to those CDRH3 regions analyzed from the current inventionand from Knappik et al. are composed of an “XYZ” codon in Lee et al. TheXYZ codon of Lee et al. is a degenerate codon with the following basecompositions:

position 1 (X): 19% A, 17% C, 38% G, and 26% T;

position 2 (Y): 34% A, 18% C, 31% G, and 17% T; and

position 3 (Z): 24% G and 76% T.

When the approximately 2% of codons encoding stop codons are excluded(these do not occur in functionally expressed human CDRH3 sequences),and the percentages are re-normalized to 100%, the following amino acidrepresentation can be deduced from the composition of the XYZ codon ofLee et al. (Table 46).

TABLE 46 Composition of CDRH3 of Lee et al., Based on the Composition ofthe Degenerate XYZ Codon. Type Percent A 6.99% C 6.26% D 10.03% E 3.17%F 3.43% G 12.04% H 4.49% I 2.51% K 1.58% L 4.04% M 0.79% N 5.02% P 3.13%Q 1.42% R 6.83% S 9.35% T 3.49% V 6.60% W 1.98% Y 6.86%

The occurrences of each of the 400 amino acid pairs, in each of the IP1,IP2, and IP3 configurations, can be computed for Knappik et al. and Leeet al. by multiplying together the individual amino acid compositions.For example, for Knappik et al., the occurrence of YS pairs in thelibrary is calculated by multiplying 15% by 4.1%, to yield 6.1%; notethat the occurrence of SY pairs would be the same. Similarly, for theXYZ codon-based libraries of Lee et al., the occurrence of YS pairswould be 6.86% (Y) multiplied by 9.35% (S), to give 6.4%; the same,again, for SY.

For the human CDRH3 sequences, the calculation is performed by ignoringthe last five amino acids in the Kabat definition. By ignoring theC-terminal 5 amino acids of the human CDRH3, these sequences may becompared to those of Lee et al., based on the XYZ codons. While Lee etal. also present libraries with “NNK” and “NNS” codons, the pair-wisecompositions of these libraries are even further away from human CDRH3pair-wise composition. The XYZ codon was designed by Lee et al. toreplicate, to some extent, the individual amino acid type biasesobserved in CDRH3.

An identical approach was used for the libraries of the invention, afterusing the methods described above to produce sample sequences. While itis possible to perform these calculations with all sequences in thelibrary, independent random samples of 10,000 to 20,000 members gaveindistinguishable results. The numbers reported herein were thusgenerated from samples of 50,000 members.

Three tables were generated for IP1, IP2 and IP3, respectively (Tables47, 48, and 49). Out of the 400 pairs, a selection from amongst the 20most frequently occurring is included in the tables. The sample of about1,000 human sequences (Lee et al., 2006) is denoted as “Preimmune,” asample of about 2,500 sequences (Jackson et al., 2007) is denoted as“Humabs,” and the more affinity matured subset of the latter, whichexcludes all of the Preimmune set, is denoted as “Matured.” Syntheticlibraries in the art are denoted as HuCAL (Knappik, et al., 2000) andXYZ (Lee et al., e 2004). Two representative libraries of the inventionare included: LUA-59 includes 59 N1 segments, 278 DH segments, 141 N2segments, and 28 H3-JH segments (see Examples, above). LUA-141 includes141 N1 segments, 278 DH segments, 141 N2 segments, and 28 H3-JH segments(see Examples, above). Redundancies created by combination of the N1 andtail sequences were removed from the dataset in each respective library.In certain embodiments, the invention may be defined based on thepercent occurrence of any of the 400 amino acid pairs, particularlythose in Tables 47-49. In certain embodiments, the invention may bedefined based on at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, or more of these pairs. In certain embodimentsof the invention, the percent occurrence of certain pairs of amino acidsmay fall within ranges indicated by “LUA−” (lower boundary) and “LUA+”(higher boundary), in the following tables. In some embodiments of theinvention, the lower boundary for the percent occurrence of any aminoacid pairs may be about 0.1, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2,2.25, 2.5, 2.75, 3, 3.25, 3.5, 3.75, 4, 4.25, 4.5, 4.75, and 5. In someembodiments of the invention, the higher boundary for the percentoccurrence of any amino acid pairs may be about 0.1, 0.25, 0.5, 0.75, 1,1.25, 1.5, 1.75, 2, 2.25, 2.5, 2.75, 3, 3.25, 3.5, 3.75, 4, 4.25, 4.5,4.75, 5, 5.25, 5.5, 5.75, 6, 6.25, 6.5, 6.75, 7, 7.25, 7.5, 7.75, and 8.According to the present invention, any of the lower boundaries recitedmay be combined with any of the higher boundaries recited, to establishranges, and vice-versa.

TABLE 47 Percent Occurrence of i − i + 1 (IP1) Amino Acid Pairs in HumanSequences, Exemplary Libraries of the Invention, and the Libraries ofKnappik et al. and Lee et al. LUA- LUA- Pairs Preimmune Humabs Matured59 141 HuCAL XYZ LUA− LUA+ Range HuCAL XYZ YY 5.87 4.44 3.27 5.83 5.932.25 0.47 2.50 6.50 4.00 0 0 SG 3.54 3.41 3.26 3.90 3.72 0.61 1.13 2.504.50 2.00 0 0 SS 3.35 2.65 2.26 2.82 3.08 0.16 0.88 2.00 4.00 2.00 0 0GS 2.59 2.37 2.20 3.82 3.52 0.61 1.13 1.50 4.00 2.50 0 0 GY 2.55 2.342.12 3.15 2.56 2.25 0.83 2.00 3.50 1.50 1 0 GG 2.19 2.28 2.41 6.78 3.512.25 1.45 2.00 7.00 5.00 1 0 YS 1.45 1.30 1.23 1.40 1.52 0.61 0.64 0.752.00 1.25 0 0 YG 1.35 1.21 1.10 1.64 1.69 2.25 0.83 0.75 2.00 1.25 0 1SY 1.31 1.07 0.90 1.65 1.77 0.61 0.64 0.75 2.00 1.25 0 0 YD 1.67 1.401.17 0.88 0.90 0.61 0.69 0.75 2.25 1.50 0 0 DS 1.53 1.31 1.16 1.20 1.460.16 0.94 0.75 2.00 1.25 0 1 DY 1.40 1.23 1.11 0.34 0.48 0.61 0.69 0.252.00 1.75 1 1 VV 1.37 0.94 0.64 2.30 2.30 0.16 0.44 0.50 2.50 2.00 0 0GD 1.20 1.21 1.25 0.49 0.44 0.61 1.21 0.25 1.75 1.50 1 1 AA 1.16 0.930.75 1.27 1.46 0.16 0.49 0.60 1.50 0.90 0 0 RG 1.08 1.26 1.38 1.69 1.380.61 0.82 1.00 2.00 1.00 0 0 VA 0.91 0.66 0.46 0.36 0.35 0.16 0.46 0.251.00 0.75 0 1 GV 0.84 0.89 0.95 2.87 2.16 0.61 0.79 0.80 3.00 2.20 0 0CS 0.82 0.55 0.38 0.79 0.80 0.04 0.59 0.50 1.00 0.50 0 1 GR 0.74 0.901.00 1.01 0.79 0.61 0.82 0.70 1.25 0.55 0 1 The pairs in bold compriseabout 19% to about 24% of occurrences (among the possible 400 pairs) forthe Preimmune (Lee, et al., 2006), Humabs (Jackson, et al., 2007) andmatured (Jackson minus Lee) sets. They account for about 27% to about31% of the occurrences in the LUA libraries, but only about 12% in theHuCAL library and about 8% in the “XYZ” library. This is a reflection ofthe fact that pair-wise biases do exist in the human and LUA libraries,but not in the others. The last 2 columns indicate whether thecorresponding pair-wise compositions fall within the LUA− and LUA+boundaries: 0 if outside, 1 if within.

TABLE 48 Percent Occurrence of i − i + 2 (IP2) Amino Acid Pairs in HumanSequences, Exemplary Libraries of the Invention, and the Libraries ofKnappik et al. and Lee et al. LUA- LUA- Pairs Preimmune Humabs Matured59 141 HuCAL XYZ LUA− LUA+ Range HuCAL XYZ YY 3.57 2.59 1.78 2.99 3.112.25 0.47 2.5 4.5 2 0 0 GY 3.34 2.91 2.56 4.96 3.78 2.25 0.83 2.5 5.5 30 0 SY 2.94 2.41 2.01 3.03 3.42 0.61 0.64 2 4 2 0 0 YS 2.88 2.34 1.953.24 3.32 0.61 0.64 1.75 3.75 2 0 0 SG 2.60 2.29 2.05 2.84 2.96 0.611.13 2 3.5 1.5 0 0 SS 2.27 2.01 1.84 2.30 2.50 0.16 0.88 1.5 3 1.5 0 0GS 2.16 2.12 2.10 2.96 2.32 0.61 1.13 1.5 3 1.5 0 0 GG 1.92 2.25 2.446.23 3.68 2.25 1.45 1.5 7 5.5 1 0 YG 1.17 1.14 1.15 1.39 1.47 2.25 0.831 2 1 0 0 DS 2.03 1.67 1.40 1.21 1.48 0.16 0.94 1 2.5 1.5 0 0 YD 1.711.39 1.11 0.89 0.92 0.61 0.69 0.75 1.75 1 0 0 VG 1.35 1.17 1.01 1.751.54 0.61 0.79 1 2 1 0 0 DY 1.06 1.02 0.99 0.23 0.40 0.61 0.69 0.2 1.2 11 1 WG 1.06 0.76 0.53 0.85 0.91 0.61 0.24 0.75 1.25 0.5 0 0 RY 0.98 1.000.96 0.70 0.91 0.61 0.47 0.6 1 0.4 1 0 GC 0.97 0.75 0.64 0.94 0.81 0.150.75 0.5 1 0.5 0 1 DG 0.95 1.05 1.08 1.78 1.05 0.61 1.21 0.75 2 1.25 0 1GD 0.94 0.88 0.86 0.47 0.36 0.61 1.21 0.25 1 0.75 1 0 VV 0.94 0.59 0.350.95 0.90 0.16 0.44 0.5 1 0.5 0 0 AA 0.90 0.73 0.59 0.72 0.74 0.16 0.490.5 1 0.5 0 0 The pairs in bold comprise about 18% to about 23% ofoccurrences (among the possible 400 pairs) for the Preimmune (Lee, etal., 2006), Humabs (Jackson, et al., 2007) and matured (Jackson minusLee) sets. They account for about 27% to about 30% of the occurrences inthe LUA libraries, but only about 12% in the HuCAL library and about 8%in the “XYZ” library. Because of the nature of the construction of thecentral loops in the HuCAL and XYZ libraries, these numbers are the samefor the IP1, IP2, and IP3 pairs. The last 2 columns indicate whether thecorresponding pair-wise compositions fall within the LUA− and LUA+boundaries: 0 if outside, 1 if within.

TABLE 49 Percent Occurrence of i − i + 2 (IP3) Amino Acid Pairs in HumanSequences, Exemplary Libraries of the Invention, and the Libraries ofKnappik et al. and Lee et al. LUA- LUA- Pairs Preimmune Humabs Matured59 141 HuCAL XYZ LUA− LUA+ Range HuCAL XYZ GY 3.55 2.85 2.32 5.80 4.422.25 0.83 2.5 6.5 4 0 0 SY 3.38 3.01 2.67 3.78 4.21 0.61 0.64 1 5 4 0 0YS 3.18 2.56 2.05 3.20 3.33 0.61 0.64 2 4 2 0 0 SS 2.26 1.74 1.37 1.812.18 0.16 0.88 1 3 2 0 0 GS 2.23 2.13 2.00 4.60 3.33 0.61 1.13 2 5 3 0 0YG 2.14 1.65 1.35 2.69 2.79 2.25 0.83 1.5 3 1.5 1 0 YY 1.86 1.48 1.121.18 1.27 2.25 0.47 0.75 2 1.25 0 0 GG 1.60 1.87 2.11 4.73 2.84 2.251.45 1.5 5 3.5 1 0 SG 0.90 1.04 1.12 0.93 1.25 0.61 1.13 0.75 1.5 0.75 01 DG 2.01 1.94 1.84 2.51 2.03 0.61 1.21 1.5 3 1.5 0 0 DS 1.48 1.31 1.220.41 0.55 0.16 0.94 0.25 1.5 1.25 0 1 VA 1.18 0.83 0.55 1.48 1.46 0.160.46 0.5 2 1.5 0 0 AG 1.13 1.09 1.03 0.97 1.04 0.61 0.84 0.9 2 1.1 0 0TY 1.05 0.90 0.76 1.01 1.16 0.61 0.24 0.75 1.75 1 0 0 PY 1.02 0.88 0.791.23 0.86 0.61 0.21 0.75 1.75 1 0 0 RS 1.02 0.88 0.77 0.38 0.55 0.160.64 0.25 1.25 1 0 1 RY 1.02 1.12 1.14 0.68 0.88 0.61 0.47 0.65 1.25 0.60 0 LY 1.01 0.88 0.75 0.69 0.76 0.61 0.28 0.65 1.25 0.6 0 0 DY 0.93 0.840.77 0.72 0.95 0.61 0.69 0.7 1.3 0.6 0 0 GC 0.90 0.62 0.48 0.86 0.680.15 0.75 0.5 1 0.5 0 1 The pairs in bold comprise about 18% to about23% of occurrences (among the possible 400 pairs) for the Preimmune(Lee, et al., 2006), Humabs (Jackson, et al., 2007) and matured (Jacksonminus Lee) sets. They account for 26% to 29% of the occurrences in theLUA libraris, but only about 12% in the HuCAL library and about 8% forthe “XYZ” library. Because of the nature of the construction of thecentral loops in the HuCAL and XYZ libraries, these numbers are the samefor the IP1, IP2, and IP3 pairs. The last 2 columns indicate whether thecorresponding pair-wise compositions fall within the LUA− and LUA+boundaries: 0 if outside, 1 if within.

The analysis provided in this example demonstrates that the compositionof the libraries of the present invention more closely mimics thecomposition of human sequences than other libraries known in the art.Synthetic libraries of the art do not intrinsically reproduce thecomposition of the “central loop” portion actual human CDRH3 sequencesat the level of pair percentages. The libraries of the invention have amore complex pair-wise composition that closely reproduces that observedin actual human CDRH3 sequences. The exact degree of this reproductionversus a target set of actual human CDRH3 sequences may be optimized,for example, by varying the compositions of the segments used to designthe CDRH3 libraries. Moreover, it is also possible to utilize thesemetrics to computationally design libraries that exactly mimic thepair-wise compositional prevalence found in human sequences.

Example 14 Information Content of Exemplary Libraries

One way to quantify the observation that certain libraries, orcollection of sequences, may be intrinsically more complex or “lessrandom” than others is to apply information theory (Shannon, Bell Sys.Tech. J., 1984, 27: 379; Martin et al., Bioinformatics, 2005, 21: 4116;Weiss et al., J. Theor. Biol., 2000, 206: 379, each incorporated byreference in its entirety). For example, a metric can be devised toquantify the fact that a position with a fixed amino acid representsless “randomness” than a position where all 20 amino acids may occurwith equal probability. Intermediate situations should lead, in turn, tointermediate values of such a metric. According to information theorythis metric can be represented by the formula:

I=Σ _(i=1) ^(N) f _(i) log₂ f

Here, f_(i) is the normalized frequency of occurrence of i, which may bean amino acid type (in which case N would be equal to 20). When allf_(i) are zero except for one, the value of I is zero. In any other casethe value of I would be smaller, i.e., negative, and the lowest value isachieved when all f_(i) values are the same and equal to N. For theamino acid case, N is 20, and the resulting value of I would be −4.322.Because I is defined with base 2 logarithms, the units of I are bits.

The I value for the HuCAL and XYZ libraries at the single position levelmay be derived from Tables 45 and 46, respectively, and are equal to−4.08 and −4.06. The corresponding single residue frequency occurrencesin the non-limiting exemplary libraries of the invention and the sets ofhuman sequences previously introduced, taken within the “central loop”as defined above, are provided in Table 50.

TABLE 50 Amino Acid Type Frequencies in Central Loop Type PreimmuneHumabs Matured LUA-59 LUA-141 A 5.46 5.51 5.39 5.71 6.06 C 1.88 1.461.22 1.33 1.34 D 7.70 7.51 7.38 4.76 5.23 E 2.40 2.90 3.28 3.99 4.68 F2.29 2.60 2.81 1.76 2.17 G 14.86 15.42 15.82 24.90 18.85 H 1.46 1.792.01 0.20 0.67 I 3.71 3.26 2.99 3.99 4.34 K 1.06 1.27 1.44 0.21 0.67 L4.48 4.84 5.16 4.12 4.54 M 1.18 1.03 0.93 0.94 1.03 N 1.81 2.43 2.840.41 0.65 P 4.12 4.10 4.13 5.68 3.96 Q 1.60 1.77 1.95 0.21 0.68 R 5.055.90 6.41 3.35 4.11 S 12.61 11.83 11.37 11.18 12.77 T 4.59 5.11 5.474.36 4.95 V 6.21 5.55 5.12 8.13 7.67 W 2.79 2.91 3.07 1.57 1.98 Y 14.7412.81 11.24 13.20 13.63The information content of these sets, computed by the formula givenabove, would then be −3.88, −3.93, −3.96, −3.56, and −3.75, for thepreimmune, human, matured, LUA-59 and LUA-141 sets, respectively. As thefrequencies deviate more from completely uniform (5% for each of the20), then numbers tend to be larger, or less negative.

The identical approach can be used to analyze pair compositions, orfrequencies, by calculating the sum in the formula above over the 20×20or 400 values of the frequencies for each of the pairs. It can be shownthat any pair frequency made up of the simple product of two singletonfrequency sets is equal to the sum of the individual singleton I values.If the two singleton frequency sets are the same or approximately so,this means that I (independent pairs)=2*I (singles). It is thus possibleto define a special case of the mutual information, MI, for a generalset of pair frequencies as MI (pair)=I(pair)−2*I (singles) to measurethe amount of information gained by the structure of the pairfrequencies themselves (compare to the standard definitions in Martin etal., 2005, for example, after considering that I (X)=−H(X) in theirnotation). When there is no such structure, the value of MI is simplyzero.

Values of MI computed from the pair distributions discussed above (overthe entire set of 400 values) are given in Table 51.

TABLE 51 Mutual Information Within Central Loop of CDRH3 Library or Seti - i + 1 i - i + 2 i - i + 3 Preimmune 0.226 0.192 0.163 Humabs 0.1530.128 0.111 Matured 0.124 0.107 0.100 LUA-59 0.422 0.327 0.278 LUA-1410.376 0.305 0.277 HuCAL 0.000 0.000 0.000 XYZ 0.000 0.000 0.000It is notable that the MI values decrease within sets of human sequencesas those sequences undergo further somatic mutation, a process that overmany independent sequences is essentially random. It is also worthnoting that the MI values decrease as the pairs being considered sitfurther and further apart, and this is the case for both sets of humansequences, and exemplary libraries of the invention. In both cases, asthe two amino acids in a pair become further separated the odds of theirstraddling an actual segment (V, D, J plus V-D or D-J insertions)increase, and their pair frequencies become closer to a simple productof singleton frequencies.

Table 52 contains sequence information on certain immunoglobulin genesegments cited in the application. These sequences are non-limiting, andit is recognized that allelic variants exist and encompassed by thepresent invention. Accordingly, the methods present herein can beutilized with mutants of these sequences.

TABLE 52 Sequence Information for Certain Immunoglobulin Gene Segments Cited Herein SEQ ID NO: SequencePeptide or Nucleotide Sequence Observations 423 IGHV1-3QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKYSQKFQGRVTITRDTSAST AYMELSSLRSEDTAVYYCAR 424IGHV1-8_v1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYDINWVRQATGQGLEWMGWMNPNSGNTGYAQKFQGRVTMTR NTS IS TAYMELSSLRSEDTAVYYCAR 425IGHV1-8_v2 QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYDINWVRQ N to D mutation avoids NTS ATGQGLEWMGWMNPNSGNTGYAQKFQGRVTMTR DTS ISpotential glycosylation site in the TAYMELSSLRSEDTAVYYCARoriginal germline sequence (v1 above). XTS, where X is not N,and NTZ, where Z is not S or T are also options. NPS is yet anotheroption that is much less likely to  be N-linked glycosylated. 426IGHV1-24 QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKGLEWMGGFDPEDGETIYAQKFQGRVTMTEDTSTDT AYMELSSLRSEDTAVYYCAT 427IGHV1-45 QMQLVQSGAEVKKTGSSVKVSCKASGYTFTYRYLHWVRQAPGQALEWMGWITPFNGNTNYAQKFQDRVTITRDRSMST AYMELSSLRSEDTAMYYCAR 428IGHV1-58 QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTA YMELSSLRSEDTAVYYCAA 429 IGHV2-5QITLKESGPTLVKPTQTLTLTCTFSGFSLSTSGVGVGWIRQPPGKALEWLALIYWDDDKRYSPSLKSRLTITKDTSKNQVVL TMTNMDPVDTATYYCAHR 430IGHV2-26 QVTLKESGPVLVKPTETLTLTCTVSGFSLSNARMGVSWIRQPPGKALEWLAHIFSNDEKSYSTSLKSRLTISKDTSKSQVVLT MTNMDPVDTATYYCARI 431IGHV2-70_v1  RVTLRESGPALVKPTQTLTLTCTFSGFSLSTSGM C VSWIRQPPGKALEWLARIDWDDDKYYSTSLKTRLTISKDTSKNQVVL TMTNMDPVDTATYYCARI 432IGHV2-70_v2  RVTLRESGPALVKPTQTLTLTCTFSGFSLSTSGM G VSWIRQ C to G mutation avoids unpairedPPGKALEWLARIDWDDDKYYSTSLKTRLTISKDTSKNQVVL  Cys in v1 above. G was chosenTMTNMDPVDTATYYCARI by analogy to other germlinesequences, but other amino acid types, R, S, T, as non-limitingexamples, are possible. 433 IGHV3-9EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTISRDNAKNSL YLQMNSLRAEDTALYYCAKD 434IGHV3-11 QVQLVESGGGLVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSYISSSGSTIYYADSVKGRFTISRDNAKNSLY LQMNSLRAEDTAVYYCAR 435IGHV3-13 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYDMHWVRQATGKGLEWVSAIGTAGDTYYPGSVKGRFTISRENAKNSLYL QMNSLRAGDTAVYYCAR 436 IGHV3-20EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSGINWNGGSTGYADSVKGRFTISRDNAKN SLYLQMNSLRAEDTALYHCAR 437IGHV3-21 EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLY LQMNSLRAEDTAVYYCAR 438IGHV3-43 EVQLVESGGWVQPGGSLRLSCAASGFTFDDYTMHWVRQAPGKGLEWVSLISWDGGSTYYADSVKGRFTISRDNSKNSL YLQMNSLRTEDTALYYCAKD 439IGHV3-49 EVQLVESGGGLVQPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSKSI AYLQMNSLKTEDTAVYYCTR 440IGHV3-53 EVQLVESGGGLIQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSVIYSGGSTYYADSVKGRFTISRDNSKNTLYL QMNSLRAEDTAVYYCAR 441 IGHV3-64EVQLVESGGGLVQPGGSLRLSCSASGFTFSSYAMHWVRQAPGKGLEYVSAISSNGGSTYYADSVKGRFTISRDNSKNTLY LQMSSLRAEDTAVYYCVK 442IGHV3-66 EVQLVESGGGLVQPGGSLRLSCAASGFTVSSNYMSVVVRQAPGKGLEWVSVIYSGGSTYYADSVKGRFTISRDNSKNTLYL QMNSLRAEDTAVYYCAR 443 IGHV3-72EVQLVESGGGLVQPGGSLRLSCAASGFTFSDHYMDWVRQAPGKGLEWVGRTRNKANSYTTEYAASVKGRFTISRDDSKN SLYLQMNSLKTEDTAVYYCAR 444IGHV3-73 EVQLVESGGGLVQPGGSLKLSCAASGFTFSGSAMHWVRQASGKGLEWVGRIRSKANSYATAYAASVKGRFTISRDDSKN TAYLQMNSLKTEDTAVYYCTR 445IGHV3-74 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMHWVRQAPGKGLVWVSRINSDGSSTSYADSVKGRFTISRDNAKNT LYLQMNSLRAEDTAVYYCAR 446IGHV4-4v1 QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSNWWSVVVRContains CDRH1 with size 6 QPPGKGLEWIGEIYHSGSTNYNPSLKSRVTISVDKSKNQFS (Kabat definition); canonical LKLSSVTAADTAVYYCARstructure H1-2. Sequence corresponds to allele *02 of IGHV4-4. 447IGHV4-4v2 QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPContains CDRH1 with size 5 AGKGLEWIGRIYTSGSTNYNPSLKSRVTMSVDTSKNQFSL(Kabat definition); canonical KLSSVTAADTAVYYCAR structure H1-1. Sequencecorresponds to allele *07 of IGHV4-4 448 IGHV4-28QVQLQESGPGLVKPSDTLSLTCAVSGYSISSSNWWGWIRQPPGKGLEWIGYIYYSGSTYYNPSLKSRVTMSVDTSKNQF SLKLSSVTAVDTAVYYCAR 449 IGHV6-1QVQLQQSGPGLVKPSQTLSLTCAISGDSVSSNSAAWNWIRQSPSRGLEWLGRTYYRSKVVYNDYAVSVKSRITINPDTSKN QFSLQLNSVTPEDTAVYYCAR 450IGHV7-4-1 QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAMNWVRQAPGQGLEWMGWINTNTGNPTYAQGFTGRFVFSLDTSVST AYLQISSLKAEDTAVYYCAR 451IGKV1-06 AIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPE DFATYYCLQDYNYP 452IGKV1-08_v1  AIRMTQSPSSFSASTGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTIS C LQSE DFATYYCQQYYSYP 453IGKV1-08_v2  AIRMTQSPSSFSASTGDRVTITCRASQGISSYLAWYQQKPC to S mutation avoids unpaired GKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTIS SLQSE  Cys. in v1 above. S was chosen DFATYYCQQYYSYPby analogy to other germline sequences, but amino acid types,N, R, S, as non-limiting examples, are also possible 454 IGKV1-09DIQLTQSPSFLSASVGDRVTITCRASQGISSYLAVVYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDF ATYYCQQLNSYP 455 IGKV1-13AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDF ATYYCQQFNSYP 456 IGKV1-16DIQMTQSPSSLSASVGDRVTITCRASQGISNYLAWFQQKPGKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPE DFATYYCQQYNSYP 457 IGKV1-17DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPE DFATYYCLQHNSYP 458IGKV1-37_v1  DIQLTQSPSSLSASVGDRVTITCRVSQGISSYLNVVYRQKPGKVPKLLIYSASNLQSGVPSRFSGSGSGTDFTLTISSLQPED VATYY G QRTYNAP 459IGKV1-37_v2 DIQLTQSPSSLSASVGDRVTITCRVSQGISSYLNWYRQKPGRestores conserved Cys, missingKVPKLLIYSASNLQSGVPSRFSGSGSGTDFTLTISSLQPED in v1 above, just prior to CDRL3. VATYY C QRTYNAP 460 IGKV1D-16DIQMTQSPSSLSASVGDRVTITCRASQGISSWLAWYQQKPEKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPE DFATYYCQQYNSYP 461 IGKV1D-17NIQMTQSPSAMSASVGDRVTITCRARQGISNYLAWFQQKPGKVPKHLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPE DFATYYCLQHNSYP 462 IGKV1D-43AIRMTQSPFSLSASVGDRVTITCWASQGISSYLAWYQQKPAKAPKLFIYYASSLQSGVPSRFSGSGSGTDYTLTISSLQPE DFATYYCQQYYSTP 463IGKV1D-8_v1  VIWMTQSPSLLSASTGDRVTISCRMSQGISSYLAWYQQKPGKAPELLIYAASTLQSGVPSRFSGSGSGTDFTLTIS C LQSE DFATYYCQQYYSFP 464IGKV1D-8_v2  VIWMTQSPSLLSASTGDRVTISCRMSQGISSYLAWYQQKPC to S mutation avoids unpaired GKAPELLIYAASTLQSGVPSRFSGSGSGTDFTLTIS SLQSE  Cys. in v1 above. S was chosen DFATYYCQQYYSFPby analogy to other germline sequences, but amino acid types,N, R, S, as non-limiting examples, are also possible 465 IGKV2-24DIVMTQTPLSSPVTLGQPASISCRSSQSLVHSDGNTYLSWLQQRPGQPPRLLIYKISNRFSGVPDRFSGSGAGTDFTLKISR VEAEDVGVYYCMQATQFP 466IGKV2-29 DIVMTQTFLSLSVTRQQPASISCKSSQSLLHSDGVTYLYWYLQRPQQSPQLLTYEVSSRFSGVPDRFSGSGSGTDFTLKIS RVEAEDVGVYYCMQGTHLP 467IGKV2-30 DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKI SRVEAEDVGVYYCMQGTHWP 468IGKV2-40 DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSDDGNTYLDWYLQKPGQSPQLLIYTLSYRASGVPDRFSGSGSGTDFTLKIS RVEAEDVGVYYCMQRIEFP 469IGKV2D-26 EIVMTQTPLSLSITPGEQASMSCRSSQSLLHSDGYTYLYWFLQKARPVSTLLIYEVSNRFSGVPDRFSGSGSGTDFTLKISR VEAEDFGVYYCMQDAQD 470IGKV2D-29 DIVMTQTPLSLSVTPGQPASISCKSSQSLLHSDGKTYLYWYLQKPGQPPQLLIYEVSNRFSGVPDRFSGSGSGTDFTLKISR VEAEDVGVYYCMQSIQLP 471IGKV2D-30 DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNWDSGVPDRFSGSGSGTDFTLKI SRVEAEDVGVYYCMQGTHWP 472IGKV3D-07 EIVMTQSPATLSLSPGERATLSCRASQSVSSSYLSWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTDFTLTISSLQPE DFAVYYCQQDYNLP 473 IGKV3D-11EIVLTQSPATLSLSPGERATLSCRASQGVSSYLAVVYQQKPGQAPRLLIYDASNRATGIPARFSGSGPGTDFTLTISSLEPED FAVYYCQQRSNWH 474 IGKV3D-20EIVLTQSPATLSLSPGERATLSCGASQSVSSSYLAWYQQKPGLAPRLLIYDASSRATGIPDRFSGSGSGTDFTLTISRLEPE DFAVYYCQQYGSSP 475 IGKV5-2_v1ETTLTQSPAFMSATPGDKV NIS CKASQDIDDDMNWYQQKPGEAAIFIIQEATTLVPGIPPRFSGSGYGTDFTLTINNIESEDA AYYFCLQHDNFP 476 IGKV5-2_v2ETTLTQSPAFMSATPGDKV TIS CKASQDIDDDMNWYQQKP N to D mutation avoids NISGEAAIFIIQEATTLVPGIPPRFSGSGYGTDFTLTINNIESEDA potential glycosylation site in v1 AYYFCLQHDNFPabove. XIS, where X is not N, and NIZ, where Z is not S or T are alsooptions. NPS is yet another option that is much less likely to be N-linked glycosylated. 477 IGKV6-21EIVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWYQQKPDQSPKLLIKYASQSFSGVPSRFSGSGSGTDFTLTINSLEAED AATYYCHQSSSLP 478 IGKV6D-21EIVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWYQQKPDQSPKLLIKYASQSFSGVPSRFSGSGSGTDFTLTINSLEAED AATYYCHQSSSLP 479 IGKV7-3DIVLTQSPASLAVSPGQRATITCRASESVSFLGINLIHWYQQKPGQPPKLLIYQASNKDTGVPARFSGSGSGTDFTLTINPVE ANDTANYYCLQSKNFP 480 IGλV1-36QSVLTQPPSVSEAPRQRVTISCSGSSSNIGNNAVNWYQQLPGKAPKLLIYYDDLLPSGVSDRFSGSKSGTSASLAISGLQS EDEADYYCAAWDDSLNG 481 IGλV1-47QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRNNQRPSGVPDRFSGSKSGTSASLAISGLRS EDEADYYCAAWDDSLSG 482IGλV10-54  QAGLTQPPSVSKGLRQTATLTCTGNSNNVGNQGAAWLQQHQGHPPKLLSYRNNNRPSGISERLSASRSGNTASLTITGLQ PEDEADYYCSAWDSSLSA 483IGλV2-11_v1 QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVPDRFSGSKSGNTASLTISGL QAEDEADYYC C SYAGSYTF 484IGλV2-11_v2 QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQC to S mutation avoids unpairedQHPGKAPKLMIYDVSKRPSGVPDRFSGSKSGNTASLTISGL  Cys in v1 above. S was chosenQAEDEADYYC S SYAGSYTF by analogy to other germlinesequences, but other amino acid types, such as Q, G, A, L, as non-limiting examples, are also possible 485 IGλV2-18QSALTQPPSVSGSPGQSVTISCTGTSSDVGSYNRVSWYQQPPGTAPKLMIYEVSNRPSGVPDRFSGSKSGNTASLTISGL QAEDEADYYCSLYTSSSTF 486IGλV2-23_v1 QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGL QAEDEADYYC C SYAGSSTL 487IGλV2-23_v2 QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQ C to S mutation avoids unpairedHPGKAPKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGL Cys in v1 above. S was chosen by QAEDEADYYC S SYAGSSTLanalogy to other germline sequences, but other amino acidtypes, such as Q, G, A, L, as non- limiting examples, are also possible488 IGλV2-8 QSALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSKRPSGVPDRFSGSKSGNTASLTVSG LQAEDEADYYCSSYAGSNNF 489IGλV3-10  SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWYQQKSGQAPVLVIYEDSKRPSGIPERFSGSSSGTMATLTISGAQVED EADYYCYSTDSSGNH 490 IGλV3-12 SYELTQPHSVSVATAQMARITCGGNNIGSKAVHWYQQKPGQDPVLVIYSDSNRPSGIPERFSGSNPGNTTTLTISRIEAGD EADYYCQVWDSSSDH 491 IGλV3-16 SYELTQPPSVSVSLGQMARITCSGEALPKKYAYWYQQKPGQFPVLVIYKDSERPSGIPERFSGSSSGTIVTLTISGVQAEDE ADYYCLSADSSGTY 492 IGλV3-25 SYELMQPPSVSVSPGQTARITCSGDALPKQYAYWYQQKPGQAPVLVIYKDSERPSGIPERFSGSSSGTTVTLTISGVQAE DEADYYCQSADSSGTY 493 IGλV3-27 SYELTQPSSVSVSPGQTARITCSGDVLAKKYARWFQQKPGQAPVLVIYKDSERPSGIPERFSGSSSGTTVTLTISGAQVEDE ADYYCYSAADNN 494 IGλV3-9SYELTQPLSVSVALGQTARITCGGNNIGSKNVHWYQQKPGQAPVLVIYRDSNRPSGIPERFSGSNSGNTATLTISRAQAGD EADYYCQVWDSSTA 495 IGλV4-3LPVLTQPPSASALLGASIKLTCTLSSEHSTYTIEWYQQRPGRSPQYIMKVKSDGSHSKGDGIPDRFMGSSSGADRYLTFSN LQSDDEAEYHCGESHTIDGQVG 496IGλV4-60 QPVLTQSSSASASLGSSVKLTCTLSSGHSSYIIAWHQQQPGKAPRYLMKLEGSGSYNKGSGVPDRFSGSSSGADRYLTIS NLQLEDEADYYCETWDSNT 497IGλV5-39 QPVLTQPTSLSASPGASARFTCTLRSGINVGTYRIYWYQQKPGSLPRYLLRYKSDSDKQQGSGVPSRFSGSKDASTNAGLL LISGLQSEDEADYYCAIWYSSTS 498IGλV7-46 QAVVTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPYWFQQKPGQAPRTLIYDTSNKHSWTPARFSGSLLGGKAALTLSG AQPEDEAEYYCLLSYSGAR 499IGλV8-61 QTVVTQEPSFSVSPGGTVTLTCGLSSGSVSTSYYPSWYQQTPGQAPRTLIYSTNTRSSGVPDRFSGSILGNKAALTITGA QADDESDYYCVLYMGSGI 500IGλV9-49 QPVLTQPPSASASLGASVTLTCTLSSGYSNYKVDWYQQRPGKGPRFVMRVGTGGIVGSKGDGIPDRFSVLGSGLNRYLTI KNIQEEDESDYHCGADHGSGSNFV 501IGHD1-1 GGTACAACTGGAACGAC See (1) below. 502 IGHD1-14 GGTATAACCGGAACCAC503 IGHD1-20 GGTATAACTGGAACGAC 504 IGHD1-7 GGTATAACTGGAACTAC 505IGHD2-21_v1  AGCATATTGTGGTGGTGA T TGCTATTCC 506 IGHD2-21_v2 AGCATATTGTGGTGGTGA C TGCTATTCC Common allelic variant encoding adifferent amino acid sequence, compared to v1, in 2 of 3 forwardreading frames. 507 IGHD2-8 AGGATATTGTACTAATGGTGTATGCTATACC 508 IGHD3-16GTATTATGATTACGTTTGGGGGAGTTATGCTTATACC 509 IGHD3-9GTATTACGATATTTTGACTGGTTATTATAAC 510 IGHD4-23 TGACTACGGTGGTAACTCC 511IGHD4-4/4-11 TGACTACAGTAACTAC 512 IGHD5-12 GTGGATATAGTGGCTACGATTAC 513IGHD5-24 GTAGAGATGGCTACAATTAC 514 IGHD6-25 GGGTATAGCAGCGGCTAC 515IGHD6-6 GAGTATAGCAGCTCGTCC 516 IGHD7-27 CTAACTGGGGA (1) Each of the IGHDnucleotide sequences can be read in three (3) forward reading frames,and, possibly, in 3 reverse reading frames. For example, the nucleotidesequence given for IGHD1-1, depending on how it inserts in full V-DJrearrangement, may encode the full peptide sequences: GTTGT (SEQ ID NO:517), VQLER (SEQ ID NO: 518) and YNWND (SEQ ID NO: 519) in the forwarddirection, and VVPVV (SEQ ID NO: 520), SFQLY (SEQ ID NO: 521) and RSSCT(SEQ ID NO: 522) in the reverse direction. Each of these sequences, inturn, could generate progressively deleted segments as explained in theExamples to produce suitable components for libraries of the invention.

Example 15 Selection of Antibodies from the Library

In this example, the selection of antibodies from a library of theinvention (described in Examples 9-11 and other Examples) isdemonstrated. These selections demonstrate that the libraries of theinvention encode antibody proteins capable of binding to antigens. Inone selection, antibodies specific for “Antigen X”, a protein antigen,were isolated from the library using the methods described herein. FIG.24 shows binding curves for six clones specifically binding Antigen X,and their Kd values. This selection was performed using yeast with theheavy chain on a plasmid vector and the kappa light chain libraryintegrated into the genome of the yeast.

In a separate selection, antibodies specific for a model antigen, henegg white lysozyme (HEL) were isolated. FIG. 25 shows the binding curvesfor 10 clones specifically binding HEL; each gave a Kd>500 nM. Thisselection was performed using yeast with the heavy chain on a plasmidvector and the kappa light chain library on a plasmid vector. Thesequences of the heavy and light chains were determined for clonesisolated from the library and it was demonstrated that multiple cloneswere present. A portion of the FRM3s (underlined) and the entire CDRH3sfrom four clones are shown below (Table 53 and Table 54, the latterusing the numbering system of the invention).

TABLE 53 Sequences of CDRH3, and a Portion of FRM3, from Four HEL Binders SEQ Seq ID Name NO: FRM3 and CDRH3 TailN1 DH N2 H3-JH CR080362 523 AKGPSVPAARAEYFQH G PS VPA AR AEYFQH CR080363524 AREGGLGYYYREWYFDL E GGL GYYY RE WYFDL CR080372 525 AKPDYGAEYFQH — PDYG — AEYFQH EK080902 526 AKEIVVPSAEYFQH E — IVV PS AEYFQH

TABLE 54 Sequences of CDRH3 from Four HEL Binders in Numbering System ofthe Invention, According to the Numbering System of the Invention [Tail][N1] [DH] [N2] Clones 95 96 96A 96B 97 97A 97B 97C 97D 98 98A 98BCR080362 G P S — V P A — — A R — CR080363 E G G L G Y Y Y — R E —CR080372 — P — — D Y G — — — — — EK080902 E — — — I V V — — P S —[H3-JH] CDRH3 Clones 99E 99D 99C 99B 99A 99 100 101 102 Length CR080362— — — A E Y F Q H 14 CR080363 — — — — W Y F D L 15 CR080372 — — — A E YF Q H 10 EK080902 — — — A E Y F Q H 12 Sequence Identifiers: CR080362(SEQ ID NO: 523); CR080363 (SEQ ID NO: 524); CR080372 (SEQ ID NO: 525);EK080902 (SEQ ID NO: 526)The heavy chain chassis isolated were VH3-23.0 (for EK080902 andCR080363), VH3-23.6 (for CR080362), and VH3-23.4 (for CR080372). Thesevariants are defined in Table 8 of Example 2. Each of the four heavychain CDRH3 sequences matched a designed sequence from the exemplifiedlibrary. The CDRL3 sequence of one of the clones (ED080902) was alsodetermined, and is shown below, with the surrounding FRM regionsunderlined:

CDRL3: (SEQ ID NO: 527) YYCQESFHIPYTFGGG.In this case, the CDRL3 matched the design of a degenerate VK1-39oligonucleotide sequence in row 49 of Table 33. The relevant portion ofthis table is reproduced below, with the amino acids occupying eachposition of the isolated CDRL3 bolded and underlined:

Junc- CDR tion Degenerate SEQ Chassis Length type Oligonucleotide ID 8990 91 92 93 94 95 96 97 VK1-39 9 1 CWGSAAWCATHC 307 LQ EQ ST FSY HNPRSTIST P FY T MVTABTCCTTWC ACT

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments and methods described herein. Such equivalents are intendedto be encompassed by the scope of the following claims.

APPENDIX A GI Numbers of Kappa Light Chains Used to Derive the VKLibraries

23868 2385488 16923194 58222611 70798854 98956311 32779 2385490 1692320258222613 70798856 98956323 32810 2385492 16923208 58222615 7079885898956325 33059 2385494 17226623 58222617 70798860 98956327 33144 238549517226631 58222619 70798862 98956337 33156 2385497 17226635 5822262170798866 98956341 33170 2597932 17226639 58222623 70798868 9895634333173 2597935 17226643 58222625 70798872 98956349 33183 2597937 1722664558222627 70798874 98956355 33185 2597943 17226655 58222629 7079887898956357 33189 2597946 17381491 58222631 70798880 98956365 33191 259794817385013 58222633 70798882 98956375 33195 2597950 17385015 5822263570798884 98956379 33200 2597952 17385017 58222637 70798886 9895638133202 2599531 17385019 58222639 70798888 98956383 33221 2599533 1738502158222641 70798890 98956400 33227 2599535 17483729 58222643 7079889298956404 33230 2599545 18025561 58222645 70798894 98956406 33233 262505918025563 58222647 70798896 98956414 33237 2632152 18025573 5822264970798898 98956418 33268 2654047 18025575 58222651 70798900 9895642233288 2654051 18025577 58222653 70798902 98956426 33290 2654055 1802557958222655 70798904 98956428 33294 2773084 18025581 58222657 7079890698956430 33296 2920359 18025583 58222659 70798914 98956432 33298 299567418025585 58222661 70798916 98956436 33300 2995676 18025587 5822266370798918 98956440 33302 2995678 18025589 58222665 70798920 9902297733304 2995680 18025591 58222667 70798922 99022979 33324 2995682 1802559358222669 70798926 99022981 33330 2995688 18025595 58222671 7079892899022983 33415 2995690 18025597 58222673 70798930 99022985 33416 302313418025599 58222675 70798934 99022987 33417 3023136 18025603 5822267770798936 99022989 33418 3023138 18025605 58222679 70798940 9902299133421 3023140 18025607 58222681 70798942 99022993 33422 3023142 1802561158222683 70798946 99022995 33423 3023144 18025613 58222685 7079894899022997 33424 3023146 18025617 58222687 70798950 99022999 33426 302314818025621 58222689 70798952 99023002 33647 3251385 18025623 5822269170798954 99023004 33649 3251387 18025627 58222693 70798956 9902300633655 3251389 18025629 58222695 71058688 99023008 33657 3251391 1802563558222697 71058704 99023010 33659 3251744 18025639 58222699 7105871299023012 33665 3251749 18025641 58222701 71058717 99023474 33669 325198318025645 58222703 71058719 99023476 33679 3251985 18025651 5822270571058721 99023478 33683 3288824 18025653 58222707 71058723 9902348033685 3378165 18025655 58222709 71058725 99023482 33756 3378177 1802565758222711 71058727 99023484 34022 3378183 18025659 58222713 7105872999025082 36657 3451194 18025661 58222715 71058731 99025083 37860 360338218025665 58222717 71482591 99025084 37909 3603384 18025667 5822271971482622 99025903 38361 3603386 18025669 58222721 71482624 9902591638362 3603388 18025677 58222723 71482634 99026398 38363 3603390 1802567958222725 71482636 99026399 38367 3603392 18025681 58222727 7148263899026416 38436 3603394 18025683 58222729 71482640 99026418 38438 360339618025685 58222731 71482642 109240611 38439 3641303 18025687 5822273371482644 109240615 38440 3641307 18025689 58222735 71482646 10924061938441 3644015 18025693 58222737 71482648 109240627 38442 364402118025697 58222739 71482650 109240631 38448 3746530 18025701 5822274171482652 109240635 38485 3747011 18025705 58222743 71482654 10924063738487 3747015 18025709 58222745 71792302 109240641 38489 382108518025715 58222747 71792306 109240643 38491 3821088 18025717 5822274971792308 109240647 38493 3901025 18025719 58222751 73532341 10924065538495 3928173 18092607 58222753 75707120 109240657 38497 392818118092609 58222755 75707124 109240661 38499 3928185 18092611 5822275775707126 109240665 38501 3928189 18092613 58222759 75707128 10924066938503 3928210 18092615 58222761 75707130 109240671 38505 392821118092617 58222763 75707132 109240675 178678 3928212 18092619 5822276575707134 109240679 182338 3928214 18092621 58222767 75707138 109240687182340 3928215 18092623 58222769 75707140 109240691 182342 392821918307263 58222771 75707148 109240695 182344 3928220 18307265 5822277375707154 109240701 182346 3928222 18307267 58222775 75707156 109240705182348 3928223 18307269 58222777 75707158 109240709 183962 392822418307271 58222779 75707160 109240713 183968 3928225 18307273 5822278175707162 109240717 183972 3928227 18307275 58222783 75707168 109240721185375 3928231 18307277 58222785 75707170 109240723 185377 392823218307279 58222787 75707172 109240729 185379 3928233 18307281 5822278975707174 109240733 185381 3928234 18307283 58222791 75707176 109240737185383 3928235 18307285 58222793 75707180 109240741 185385 392823618307289 58222795 75707188 109240745 185387 3928237 18307291 5822279775707194 109240760 185389 3928238 18307293 58222799 75707196 109240764185391 3928239 18626727 58222801 75707198 109240766 185393 392824018626728 58222803 75707204 109240770 185395 3928243 18626729 5822280575707206 109241210 185397 3928244 18626730 58222807 75707208 109241212185399 3928245 18632678 58222809 75707210 109241214 185401 392824818698406 58222811 75707220 109241216 185403 3928250 19170347 5822281375707222 109241218 185415 3928251 19701578 58222815 75707226 109241220185417 3928252 19744467 58222817 75707228 109241450 185419 392825319744471 58222819 75707230 109241549 185423 3928254 19744475 5822282175707232 109241551 185427 3928257 19744479 58222823 75707234 109242373185811 3928258 19744487 58222825 75707236 109242377 185813 392825919744491 58222828 75707238 109242379 185815 3928260 19744495 5822283075707240 109242381 185816 3928261 19744499 58222832 75707242 109242383185827 3928263 19744503 58222834 75707244 109242385 185829 392826419744507 58222836 75707246 109242387 185831 3928265 19744511 5822283875707248 109242389 185833 3928266 19744515 58222840 75707250 109242395185835 3928267 19744519 58222843 75707262 109242399 185837 392827619744523 58222845 75707264 109242401 185839 3928277 19744527 5822284775707268 109242403 185841 3928278 19744531 58222849 75707270 109242409185845 3928279 19744535 58222851 75707272 109242411 185847 392828019744539 58222853 75707274 109242417 185849 3928283 19744543 5822285575707276 109242419 185855 3928287 19744547 58222857 75707278 109242421185859 3928288 19744551 58222859 75707282 109242423 185862 392828919744555 58222861 75707284 109242425 185866 3928290 19744559 5822286375707292 109242427 185868 3928291 19744563 58222865 75707298 109245190185870 3928293 19744567 58222867 75707300 109245192 185872 392829419744571 58222869 75707302 109245194 185874 3928295 19744575 5822287175707304 109693080 185880 3928296 19744579 58222873 75707306 109693082185882 3928297 19744583 58222875 75707316 109693084 185884 392829819744587 58222877 75707318 109693094 185886 3928299 20372497 5822287975707322 109693096 185888 3928301 20372499 58222881 75707324 109693100185890 3928302 20372501 58222883 75707334 109693102 185892 392830320372503 58222885 75707338 109693110 185894 3928304 20372505 5822288775707340 109693112 185896 3928308 20372507 58222889 75707362 109693114185898 3928309 20372509 58222891 75707368 109693116 185904 392831020372511 58222893 75707370 109693118 185906 3928312 20372513 5822289575707372 109693120 185908 3928315 20372515 58222897 75707374 109693135185910 3928316 20372517 58222899 75707378 109693137 185912 392831720372519 58222901 75707382 109693139 185920 3928318 20372521 5822290375707384 109693144 185922 3928319 20372523 58222905 75707386 109693146185928 3928320 20372525 58222907 75707398 109693148 185934 392832120372527 58222909 75707406 109693150 185950 3928323 20372529 5822291175707408 109693152 185980 3928324 20387057 58222913 75707410 109693154185984 3928325 20387059 58222915 75707412 109693157 185987 392832620387061 58222917 75707416 109693159 185988 3928327 21311286 5822291975707418 109693165 186008 3928329 21311288 58222923 75707420 109693167186015 3928330 21311294 58222925 75707422 109693169 186017 392833121311296 58222927 75707424 109693171 186019 3928332 21311318 5822292975707426 109693177 186040 3928333 21311322 58222931 75707428 109693179186041 3928334 21669062 58222933 75707430 109693181 186042 392833521669064 58222935 75707432 109693183 186047 3928336 21669066 5822293775707434 109693187 186199 3928337 21669068 58222939 75707444 109693189186266 3928338 21669070 58222941 75707446 109693201 254719 392833921669072 58222943 75707448 109693203 257550 3928340 21669074 5822294575707454 109693206 261239 3928341 21669076 58222947 75707460 109693210265236 3928342 21669078 58222949 75707462 109693216 265240 392834321669080 58222951 75707464 109693218 298552 3928344 21669082 5822295375707472 109693220 298560 3928345 21669084 58222955 75707476 109693222298827 3928346 21669086 58222957 75707500 109693228 298829 392834721669088 58222959 75707502 109693230 299955 3928348 21669090 5822296175707504 109693232 306919 3928349 21669092 58222963 75707506 109693235306957 3928350 21669094 58222965 75707508 109693237 306959 392835121669096 58222967 75707510 109693239 306961 3928352 21669098 5822296975707514 109693241 306963 3928353 21669100 58222971 75707516 109693249306965 3928354 21669102 58222973 75707518 109693253 306967 392835521669104 58222975 75707520 109693255 306971 3928356 21669106 5822297775707522 109693261 306980 3928357 21669108 58222979 75707524 109693264306982 3928358 21669110 58222981 75707526 109942421 306984 392835921669112 58222983 75707528 109942431 306986 3928360 21669114 5822298575707530 110290934 306988 3928361 21669116 58222987 75707534 110610132306990 3928362 21669118 58222989 75707536 110624509 306992 392836321669120 58222991 75707540 110657101 306994 3928364 21669122 5822299375707542 110657103 306996 3928365 21669124 58222995 75707544 110657105306998 3928366 21669126 58222997 75707546 110657107 307000 392836721669128 58222999 75707548 110657109 348203 3928368 21669130 5822300175707550 110657111 348205 3928369 21669132 58223003 75707552 110657113348207 3928370 21669134 58223005 75707586 110657115 348211 392837121669136 58223007 75707598 110657123 386052 3928372 21669138 5822300975707600 110657124 396631 3928373 21669140 58223011 75707602 110657125397787 3928374 21669142 58223013 75707604 110657158 397789 392837521669144 58223015 75707618 110657159 397791 3928376 21669146 5822301776058957 110657160 397793 3928377 21669148 58223019 76252624 110657161397795 3928378 21727250 58223021 76252626 110657162 398490 392837921998806 58223023 76252630 110657163 398491 3928380 21998808 5822302576252632 110657164 398492 3928381 21998810 58223027 76252634 110657165404110 3928382 21998812 58223029 76252636 110657166 404112 392838321998814 58223031 76252638 110657167 404114 3928384 21998816 5822303376252640 110657168 408365 3928385 21998818 58223035 76252642 110657169409042 3928386 21998820 58223037 76252644 110657170 414035 392838721998822 58223039 76252646 110657171 415651 3928388 21998824 5822304176781673 110657172 415710 3928389 21998826 58223043 77378090 110657173415955 3928390 21998830 58223045 77378092 110657174 415957 392839121998832 58223047 77378094 110657175 415959 3928392 22086572 5822304977378096 110657176 415961 3928393 22086575 58223051 77378098 110657177415963 3928394 22086581 58223053 77378100 110657178 415965 392839522086587 58223055 77378102 110657179 415967 3928396 22086593 5822305777378105 110657180 415969 3928397 22091617 58223059 77378107 110657181415971 3928398 22214019 58223061 77378109 110657182 416329 392839922214023 58223063 77378111 110657183 416331 3928400 22297542 5822306577378135 110657184 416333 3928401 22556681 58223067 77378137 110657185416335 3928402 22556683 58223069 77378139 110657186 416337 392840322556684 58223071 77378141 110657187 430845 3928404 22607990 5822307377378143 110657188 431039 3928405 22620896 58223075 77378145 110657189431040 3928406 22620899 58223077 77378147 110657230 431041 392840722640510 58223079 77378149 110657232 431042 3928408 22640512 5822308177378151 110657234 431043 3928409 22640513 58223083 77378153 110657236431044 3928410 22642789 58223085 77378155 110657238 431045 392841122642790 58223087 77378157 110657240 431046 3928412 22642791 5822308977378159 110657242 431047 3928413 22642808 58223091 77378161 110657244431048 3928414 22642809 58223093 77378163 110657246 431049 392841522642810 58223095 77378165 110657248 431051 3928416 22642811 5822309777378167 110657250 431052 3928417 22643188 58223099 77378169 110657252431053 3928418 22643190 58223101 77378172 110657254 431067 392841922643192 58223103 77378174 110657256 431069 3928420 22643196 5822310577378176 110657258 431071 3928421 22647625 58223107 77378224 110657615431073 3928422 22647633 58223109 77378225 110657617 431075 392842323194480 58223111 77378228 110657619 431077 3928424 23194500 5822311377378230 110657621 431079 3928425 23225992 58223115 77378234 110657624431081 3928426 23225994 58223117 77378236 110657676 431083 392842723225996 58223119 77378237 110657678 431085 3928428 23234613 5822312177378239 110657728 431087 3928430 23320663 58223123 77378241 110657730431089 3928431 23342423 58223125 77378245 110658341 433889 392843223343554 58223127 77378247 110660158 436562 3928433 24412754 5822312977378249 110660166 440153 3928434 24412756 58223131 77378251 110660174441312 3928435 24412758 58223133 77378253 112184495 441314 392843624474081 58223135 77378255 112184497 441316 3928437 24850297 5822313777379405 112184499 441318 3928438 26985941 58223139 77379407 112184501441320 3928439 27368974 58223141 77379409 112184503 441322 392844027368976 58223149 77379412 112184505 441324 3928441 27368978 5822315177379414 112184507 441330 3928442 27368981 58223153 77379416 112184509441332 3928443 27368983 58223155 77379418 112184511 441334 392844427368986 58223157 77379420 112184513 441336 4100379 27368991 5822315977379422 112189154 441338 4100381 27368993 58223161 77379425 112191695441342 4100383 27368997 58223163 77379427 112191699 441344 410364427368999 58223165 77379429 112703827 441346 4103662 27369001 5822316777379431 112708249 441348 4103664 27369003 58223169 77379433 112708250441350 4103666 27369007 58223171 77379435 112711584 441352 410367427369009 58223173 77379437 112712351 441354 4128063 27369011 5822317577379439 112712352 441356 4139195 27818830 58223177 77379441 112712353441358 4139197 27867541 58223179 77379443 112712354 441360 413919927873542 58223181 77379445 112712355 441364 4139201 27875080 5822318377379447 112712356 441366 4323178 27875088 58223185 77379449 112712357441368 4323182 27875191 58223187 77379457 112712358 441370 432318627875199 58223189 77379459 112712359 441372 4323194 28611056 5822319177379461 112712360 441374 4323809 28848873 58223193 77379463 112712361441376 4323811 28883544 58223195 77379477 112712362 441378 432381328883548 58223197 77379479 112712363 441380 4323821 28883550 5822319977379481 112712364 441382 4323823 29650328 58223201 77379483 112712365441384 4323825 29650334 58223203 77379485 112712366 441386 432382929650337 58223205 77379487 112712367 441388 4323831 29650339 5822320777379489 112712368 441390 4323833 29725711 58223209 77379491 112712369441392 4323839 29725713 58223211 77379493 112712370 441394 432384129725715 58223213 77379495 112712371 441396 4323845 29725717 5822321577379497 112712372 441398 4323847 29725719 58223217 77379499 112712373441400 4323849 29725721 58223219 77379501 112712374 441402 432385129725723 58223221 77379503 112712375 441408 4323853 29725725 5822322377379505 112712376 441412 4323855 29725727 58223225 77379507 112712377441414 4323857 29725729 58223227 77379509 112712378 441416 432385929725731 58223229 77379511 112712379 441418 4323861 29725733 5822323177379513 112712380 441422 4323863 30026987 58223233 77379515 112712381441424 4323865 30258344 58223235 77379517 112712382 441426 432386930258346 58223237 77379519 112712383 441428 4323871 30793253 5822323977379521 112727205 441430 4323873 30793255 58223241 77379523 112727206441432 4323875 30793257 58223243 77379525 112727207 441434 432387730793259 58223245 77379527 112727208 441436 4323881 30793261 5822324777379529 112727209 441440 4323883 30793263 58223249 77379545 112727210441444 4323885 30793265 58223251 77994607 112727211 441446 432388730793565 58223253 77994611 112727212 441448 4323889 30793567 5822325577994615 112727213 452060 4323891 30793569 58223257 77994619 112727214452061 4323893 30793571 58223259 78629976 112727215 452062 432389530793573 58223261 78629977 112727216 452063 4323897 30841928 5822326378629978 112727217 459655 4323899 30841931 58223265 80750467 112727218460858 4323901 30841933 58223267 80975580 114155738 472970 432390330841935 58223269 80975600 114155883 472971 4323905 30841939 5822327180975604 114155884 472972 4323907 30841943 58223273 80975616 114156208472973 4323909 30841945 58223275 80975618 114207907 472974 432391130841947 58223277 80975638 114385493 472975 4323913 31879463 5822327980975642 114385505 472976 4323915 31879464 58223281 80975644 114385507487826 4323923 31879467 58223283 81020146 114385509 487827 432392731879468 58223285 81020229 114385511 493148 4323929 31879471 5822328781020258 114385513 493149 4323931 31879472 58223289 81239122 114385515493150 4323933 33021483 58223291 81251581 114385517 496044 432393533044572 58223293 81251585 114385521 496046 4323937 33044573 5822329582794837 114385537 496048 4323939 33044574 58223297 83410334 114385539496050 4323941 33044582 58223299 83697271 114385541 496053 432394533044586 58223301 83959521 114385543 496055 4323947 33051527 5822330383959523 114385545 496059 4323949 33051528 58223305 83959525 114385547496061 4323951 33070272 58223307 83959937 114385549 496063 432395333070283 58223309 83959939 114385551 496065 4323955 33070284 5822331183964685 114385553 496071 4323957 33083474 58223313 83964762 114385567496073 4323959 33083476 58223315 83964764 114385569 506420 432396133083477 58223317 83964766 114385571 506424 4323963 33083478 5822331983964768 114385573 510839 4323965 33083479 58223321 83966574 114385575510841 4323983 33083480 58223323 83966576 114385579 510843 432398933083481 58223325 83966578 114385581 510845 4323993 33083482 5822332783966655 114385583 514428 4323997 33083483 58760238 83966657 114385585514429 4323999 33085842 59890568 83966659 114385587 514430 432400533235609 59890571 83966661 114385589 514431 4324007 33235611 5989481983966663 114385591 514432 4324009 33235613 60392126 83966665 114385593514433 4324011 33235615 60616327 83966667 114385595 514434 432401333235617 60616352 83970756 114385597 515780 4324019 33235619 6065011983970763 114385599 516137 4378181 33235621 60650123 83970769 114385601516187 4378183 33235623 60734312 83970772 114385603 516198 437818533235625 61697118 84659318 114385605 516213 4378187 33235627 6185381684659320 114385607 516249 4378189 33235629 61970154 84660715 114385609516265 4378191 33235631 61970158 84660717 114385611 516316 437819333235633 61970160 84660719 114385613 545722 4378195 33304656 6197016484660720 114385615 557650 4378197 33304658 61970168 84660721 114385617557651 4378199 33304661 61970172 84660722 114385619 560677 437820133304663 61970176 84660723 114385621 560678 4378203 33355480 6197018084660725 114385623 560841 4378207 33868634 61970184 84797793 114385625560843 4378209 33868636 61970192 84797795 114385627 575228 437821133868638 61970194 84797797 114385629 575236 4378213 33868640 6197019884797799 114385631 575240 4378215 33868642 61970202 84797801 114385633575257 4378217 33868644 61970206 84797803 114385635 575261 437822133868646 61970228 84797805 114385645 587143 4378223 37287525 6200184584797807 114385647 587245 4378225 37605051 62120916 84797823 114385649587323 4378227 37694620 62120917 84797825 114385651 587325 437822937694622 62120918 84797827 114385653 587327 4378233 37694624 6212091984797857 114385655 587329 4378237 37694626 62120920 84797861 114385659587331 4378239 37694628 62120921 84797883 114385661 587333 437824337694630 62120922 84797915 114385663 587335 4378245 37694632 6212092384797929 114385665 587337 4378247 37694634 62120924 84797959 114385669587341 4378249 37694636 62120925 84797961 114385671 587343 437825137694638 62120926 84797963 114385673 587345 4378253 37694640 6212092784797979 114385675 587347 4378255 37694642 62120929 84797981 114385677587349 4378259 37694644 62120931 84797985 114385679 587351 437826137694646 62120932 84798001 114385681 587353 4378265 37694648 6212093384798003 114385683 598165 4378267 37694650 62120934 84798005 114385685598167 4378269 37694654 62120935 84798007 114385687 598170 437827137694660 62120938 84798009 114385689 598172 4378273 37694662 6212093984798011 114385691 601979 4378275 37694664 62120940 84798033 114385693601982 4378279 37694666 62120941 84798035 114385699 601984 437828137694668 62120943 84798055 114385701 609002 4378283 37694670 6212094484798057 114385703 609004 4378287 37694672 62120945 84798059 114385705619259 4378291 37694674 62120946 84798061 114385707 623043 437829337694676 62120947 84798063 114385709 624874 4378295 37694678 6212094884798103 114385711 632983 4378297 37694680 62120949 84798107 114385713632985 4378299 37694682 62120950 84798115 114385715 632987 437830137694684 62120951 84798117 114385717 633227 4378303 37694686 6212095284798147 114385719 642581 4378305 37694688 62120953 84798149 114385721681896 4378307 37694690 62120954 84798167 114385723 681899 437830937694692 62120955 84798169 114385725 685029 4378313 37694694 6212095684798171 114385727 693862 4378315 37694696 62120957 84798173 114385729722413 4378317 37694698 62120958 84798175 114385731 722417 437831937694700 62120959 84798177 114385744 722419 4378323 37694702 6212096084798179 114385746 722421 4378325 37694704 62120961 84798181 114385748722423 4378327 37694706 62120962 84798183 114385750 722425 437833137694708 62199500 84798197 114385752 722427 4378333 37694710 6242146284798199 114385756 722429 4378335 37702652 62421466 84798201 114385774722431 4378337 37732215 62720427 84798203 114385776 722433 437833937780362 62720431 84798213 114385778 722435 4378341 39103877 6272043684798215 114385780 722437 4378343 39103879 62720442 84798217 114385782722439 4378345 39103881 62720444 84798219 114385804 722441 437834739103883 62720446 84798241 114385806 722443 4378349 39103885 6272045284798249 114385808 722455 4378351 39103887 62720454 84798255 114385921722461 4378353 40231616 62720473 84798257 115268711 722463 437835940288410 62720475 84798267 115268713 722465 4378361 40288412 6272047784798269 115268880 722467 4378363 40288414 62720483 84798271 115268892722469 4378365 40288416 62860940 84798273 115268894 722471 437836740288418 62860955 84798275 115268896 722473 4378369 40388582 6286095784798277 115268898 722475 4378371 40388585 62860959 84798279 115268900722477 4378373 40388592 62860961 84798295 115268902 722479 437837540388599 62860963 84798309 115268904 722483 4378377 40647131 6286096584798321 115268906 722485 4378379 40784425 62860981 84798323 115270875722487 4378383 40784429 62860983 84798325 115270877 722489 437838540795876 62860987 84798327 116543556 722493 4378387 42541061 6286098984798343 116543560 722495 4378389 42541069 62860991 84798345 116543564722497 4378391 42794782 62860994 84798347 116546686 722503 437839342794786 62860996 84798349 116546688 722505 4378395 44829186 6286100084798351 116551153 722511 4378397 45111420 62861002 84798364 116551156722513 4378399 45386482 62861004 84798366 116551162 722515 437840146016047 62861012 84798370 116551171 722521 4558868 46093898 6286101584798372 116551175 722523 4680172 46093902 62861017 84798374 116551179722525 4759539 46093906 62861019 84798377 116551183 722529 475954346093910 62861022 84798381 116551188 722531 4759547 46575858 6286102484798383 116551192 722535 4759551 47078185 62861029 84798386 116551201722537 4759555 47154907 62861031 84798388 116551207 722539 475956347154909 62861037 84798390 116551216 722541 4759567 47154911 6286104184798397 116551226 722543 4759575 47154913 62861045 84798407 116551231722545 4759579 47154915 62861054 85632219 116551235 722549 475958347154917 62868475 85642735 116551239 722553 4759587 47154919 6286847785644222 116551244 722555 4759591 47154921 62868479 85644224 116551249722557 4759595 47271269 62999493 85644226 116551258 722559 475959947271271 63102866 85644228 116551313 722561 4761194 47271273 6310287285644230 116551317 722569 4761281 47271275 63102874 85644232 116551321722571 4761283 47271277 63102876 85644600 116551325 722573 483768647271279 63102880 85644602 116551329 722581 4837688 47271281 6310288285644604 116551333 722585 4837690 47271283 63102888 85650161 116551337722587 4837692 47271285 63102892 85650163 116551341 722591 483769447271287 63102898 85650165 116551347 722593 4837696 47271289 6310290085650167 116551351 722599 4837698 47271291 63102902 85650169 116551369722601 5006350 47271295 63102904 85650171 116551373 722603 500635447271297 63102906 85650173 116551377 722605 5006356 47271299 6310290885650175 116551381 722607 5006358 47271307 63102910 85650177 116551404722609 5006360 47271309 63102912 85650179 116551413 722615 501951047271311 63102916 85650276 116551418 732737 5019512 47271313 6310292085650278 116551422 732739 5019514 47271315 63102922 85650280 116551427732741 5019522 47271317 63102924 85657010 116551431 732743 501952449073024 63102928 85658337 116551436 732745 5019526 49073036 6310293885658632 116551446 732747 5019538 50199324 63102940 85660488 116551452758588 5081714 50199334 63102942 85660492 116551772 758598 508171650831237 63102954 85660494 116551776 758600 5081718 50844518 6310296285660497 116551780 762823 5081720 50844522 63102964 85660498 116551785773589 5081722 50844526 63102966 85660502 116551790 790442 510268050844536 63102968 86439043 116553242 790450 5419682 50844540 6310297086439047 116555276 790794 5419684 50844548 63102972 86439051 116555819790802 5419700 50844552 63102974 86439053 116555821 790810 541970250871685 63102976 86439057 116555823 791015 5419704 50871687 6310298086439061 116559889 791019 5419706 50898144 63102986 86439063 116560960791023 5419708 50898148 63102988 86439071 116634471 791027 541971050898150 63102992 86439075 116634475 791031 5419712 50898152 6310299486439081 116795086 791035 5419731 50898154 63102996 86439147 117576090809552 5419738 50898158 63102998 86439151 118143176 809553 541974050898160 63103012 86439153 118143178 809554 5524134 50898162 6310301487298995 118147088 845515 5524140 50898164 63103030 87298999 118147090845517 5524142 50898170 63103032 87299001 118147092 845519 552414451103388 63103034 87299003 118147094 845521 5524146 51103390 6310304087299007 118147096 845523 5524148 51103392 63103044 87299009 118147098845525 5524150 51103394 63103046 87299011 118147100 845527 556650751103396 63103048 87299015 118147102 845529 5578779 51103398 6310305488496317 118147104 845531 5578781 51103400 63103056 88496922 118147106845533 5578783 51103402 63103070 90092372 118147108 845535 557878551103404 63103072 90092373 118147110 854111 5578787 51103406 6310307690092374 118147112 871275 5578789 51103408 63103078 90092387 118147114871819 5578791 51103410 63103086 90092910 118147116 871823 557879351103412 63103096 90092911 118147118 882261 5578795 51103414 6310309890092912 118147120 882263 5578797 51103416 63103106 90092913 118147122882265 5578799 51103418 63103108 90823178 118147125 882267 557880151103420 63103110 90823182 118147127 882269 5578803 51103422 6310311290823186 118425771 882271 5578805 51103424 63103114 90823190 118425773882273 5578807 51103522 63103116 90823196 118425775 882275 557880951103526 63103118 90823198 118490144 882277 5578811 51103528 6310312090994745 118490148 882279 5578815 51103532 63103140 90994747 118490152882281 5690395 51103534 63103142 90994751 118490156 882283 569039951103536 63103144 92115496 119359417 882285 5690403 51103538 6310314692115497 119836694 882287 5709454 51103540 63103148 92130102 119836767882289 5731228 51103542 63103150 92130103 119838997 882291 573123251103544 63103154 92131782 119839065 882293 5731236 51103546 6310315692131783 119839355 882295 5731242 51103548 66096574 92131784 119839523882297 5731252 51103550 66096603 92131785 119841342 882299 592160851103552 66096637 92133663 119841388 882301 5921610 51103554 6671110192133665 119841425 882303 5921614 51103556 66711102 92137567 119841512882305 5921618 51103558 66711103 92140334 121309186 882307 592162051103560 66711104 92140336 124042790 882309 5921622 51103562 6671110592141530 124042792 882311 5921624 51103564 66711106 92155949 124042815882313 5921626 51103566 66711107 92157443 126146964 882315 592164051103568 66711108 92157445 126146965 882317 6110569 51103570 6671110992157453 126146966 882319 6179861 51851021 66711110 92157459 126147776882321 6179863 51949938 66711111 92157461 126147812 882323 617986553988135 66711112 92158828 126147817 882325 6179867 53988137 6671111492158980 126147952 882327 6179869 54034484 66711116 92161545 126147954882329 6492198 54145422 66711117 92249233 126147956 882331 649220054145426 66711118 92298212 126152193 894090 6492202 54145440 6671111992298539 126152196 904629 6492204 54781098 66711120 92315622 126633956913352 6648587 54781100 66711123 92315624 126633957 929640 664988954781102 66711124 92315626 126633958 929642 6649895 54781104 6671112592315628 134125852 944925 6708204 54781106 66711126 92332837 134125853950049 7012704 54781108 66711128 92332841 134125854 973411 701270654781110 66711129 92348102 134128019 973415 7024356 54781112 6671113092348670 134269772 999107 7160978 54781126 66711131 92349881 1342730231020008 7673384 54781129 66711132 92360819 145850477 1020012 767338854781202 66711133 92370888 145850518 1020016 7673392 54781204 6671113492381676 145850519 1070309 7745134 54781206 66711135 92496960 1458505201070313 8250280 54781208 66711136 92520581 145850521 1070315 877787054781213 66711137 92520583 145850522 1070317 8777874 54781216 6671113892520584 145850523 1070321 8777878 54781218 66711139 92520586 1458505241070325 8777880 54781220 66711140 92575636 145850525 1070327 877788454781223 66711141 92589636 145850526 1070347 8777888 54781225 6671114292589637 145850527 1136554 8777890 54781227 66711143 92589638 1458505281136556 8777892 54781229 66711144 92589639 145850529 1208913 929527854781231 66711145 92589640 145850530 1235764 9295280 55274149 6671114692589641 145850531 1235766 9295282 55274153 66711147 92589642 1458505321235768 9295284 55274159 67509857 92589643 145850533 1235770 929528655274163 67509861 92589644 145850534 1235772 9295290 55824376 6814812692589645 145850535 1235774 9295292 56118076 68148140 92589646 1458505361245380 9295296 56118080 68148142 92589647 145850537 1245382 929529856292538 68148144 92589648 145850558 1255605 9295300 56294837 6814815092589649 145850561 1255607 9437312 56294841 68148152 92589650 1458505631255608 9927567 56399565 68148154 92589651 145854440 1255609 992820856609227 68148158 92589652 145856824 1255612 9968441 56609228 6814816092589653 145859735 1292860 9968443 56609229 68148164 92589656 1483555171292862 9968486 56609230 68148166 92600475 148355518 1353813 996848856609232 68148174 92600479 148355519 1353815 9968490 56609235 7079781892600487 148355520 1353817 9968492 56742105 70797820 92607622 1483555211353819 9968494 56742106 70797822 92667306 148355522 1353821 996849658003567 70797824 92667307 148355523 1353825 9968498 58003568 7079782692667308 148355524 1353827 9968500 58003569 70797828 92667309 1483555251353831 9997457 58003570 70797830 92667310 148355526 1370131 1063652458003571 70797832 92667329 148355527 1370135 11229436 58003572 7079783492667331 148355528 1370137 11343336 58003573 70797836 92798195 1483555291495627 11343337 58003587 70797838 92798196 148355530 1495628 1187671858003588 70797842 92798197 148355531 1495629 11876734 58003589 7079784492798198 148355532 1495630 11876735 58003608 70797846 92798199 1483555331495631 11876736 58003609 70797850 92798218 148540957 1495632 1187673758003610 70797852 92798220 148578450 1495633 11876738 58003611 7079785492824835 148578452 1495634 11876739 58003612 70797856 92834676 1485784541495635 11876740 58003613 70797858 92835832 148578455 1495637 1187674158003614 70797860 92835834 148578456 1495638 11878173 58003615 7079786692835836 148578457 1495639 11878175 58003616 70797870 92839400 1485784581495640 11878177 58003618 70797872 92839402 148578460 1495641 1199207558003619 70797874 92839403 149849068 1495642 11992193 58003620 7079787692839404 149849080 1495643 12003249 58003622 70797878 92839405 1498490841495644 12003251 58003623 70797884 92839406 149849088 1495645 1200325358003624 70797886 92839407 150447881 1495646 12003255 58003625 7079788892839408 150447883 1495647 12003257 58003626 70797890 92839409 1504478851495648 12655491 58003627 70797894 92845038 150447887 1495649 1265549358003628 70797898 92845490 150450134 1495650 12655500 58003629 7079860192845651 150450135 1495651 12655502 58003630 70798603 92855396 1504501361495652 12655504 58003631 70798605 92855400 150450137 1532001 1265551958003632 70798607 92855404 150450138 1532002 12655521 58003633 7079860992855408 150450139 1532027 12655525 58003634 70798611 92855412 1504501401552277 12655527 58003656 70798613 92855416 150450636 1552283 1265552958003657 70798615 92855420 150453145 1552285 12655531 58003658 7079861792855424 150453147 1552287 12655541 58003659 70798619 92855428 1504531491552291 12655558 58003660 70798621 92855432 150453151 1552295 1265556558003661 70798623 92855436 150453153 1552299 12655567 58032596 7079862792855441 150453154 1552319 12655569 58032603 70798629 92855444 1504531551561601 12655643 58032606 70798631 92856854 150453156 1561605 1265565558194104 70798633 92856855 150453157 1561607 12655662 58194120 7079863592856859 150453159 1561609 12655665 58194136 70798637 92857001 1504531611561611 12655672 58202701 70798639 92857003 150453163 1572702 1265571358202709 70798641 92857012 150453165 1572704 12655723 58202711 7079864392857016 150453167 1572706 12655730 58202713 70798645 92857018 1504531691572708 12655732 58202715 70798649 92858156 150453171 1572710 1265573658202717 70798653 92861312 150453174 1657324 12655738 58202719 7079865592861313 150453213 1657326 12655740 58202721 70798657 92861314 1504532161657328 12655748 58202723 70798659 92862784 153590356 1673592 1265575158202725 70798661 92875826 153590359 1673602 12710669 58202727 7079866792878541 153590361 1710418 12710671 58202729 70798669 92878543 1535903631770403 12734084 58202733 70798671 92878545 153590365 1770415 1273408958202735 70798673 92903931 153590367 1773056 12750933 58202737 7079867592905358 153590371 1778125 12836990 58222454 70798677 92905360 1561492231785869 12957385 58222456 70798679 92905362 156149224 1785873 1295738758222458 70798681 94034254 156149225 1785877 13170940 58222460 7079868394034257 156229617 1800286 13170944 58222462 70798685 94034261 1565573871813653 13170948 58222464 70798687 94034264 156557389 1813655 1317133358222466 70798690 94034267 156557391 1813657 13171339 58222468 7079869294034271 156557393 1834498 13171341 58222470 70798694 94034285 1565573991834563 13171343 58222473 70798696 94034316 156557403 1834564 1344799658222476 70798698 94034339 156557405 1835872 13448000 58222478 7079870094034342 156557407 1835873 13448002 58222480 70798702 94034384 1565574111839291 13448004 58222482 70798706 94034387 156562058 1864110 1344800658222484 70798708 94034390 157087534 1864112 13448010 58222487 7079871094034393 157896695 1864114 13448012 58222489 70798712 94035272 1578966971864116 13448016 58222491 70798716 94035284 157903220 1864118 1344801858222493 70798718 94035289 158055245 1864136 13448022 58222497 7079872094035298 158055254 1864138 13549147 58222499 70798722 94035300 1580552681890131 13785652 58222501 70798724 94035312 158055282 1890133 1393924558222503 70798732 94469910 158055285 1905798 13939277 58222505 7079873494469912 158055288 1905937 13939331 58222507 70798736 94469914 1580584411905941 13991697 58222509 70798738 94469922 158731523 1911732 1415069658222511 70798742 94469924 158731524 1922370 14150698 58222513 7079874494469926 158731525 1922438 14290262 58222515 70798750 95007504 1587315261922466 14573212 58222517 70798752 95007510 158731527 1922501 1457321458222519 70798758 95007512 158731528 1922528 14573216 58222521 7079876095007514 158731529 1922535 14573218 58222523 70798764 95007516 1587315301922602 14573220 58222525 70798766 95007518 158731531 1922618 1457322258222527 70798768 95007520 158731532 1922645 14573226 58222529 7079877095007522 158731533 1922679 14573254 58222531 70798772 95007524 1587315341922796 14573256 58222533 70798774 95007526 158731536 1922805 1457325858222535 70798776 95007528 158731538 1932772 14573260 58222537 7079877895007530 158731539 1943727 14573262 58222539 70798780 95007532 1587315402058533 14573264 58222541 70798782 95007534 158731541 2058535 1457326658222543 70798784 95007536 158731542 2058678 14573268 58222545 7079878695007538 158731545 2072271 14573270 58222547 70798788 95007540 1587315462072273 14573272 58222549 70798792 95007542 158731547 2072279 1457327458222551 70798794 95007544 158731548 2072981 14573276 58222553 7079879695101759 158731550 2078359 14573278 58222556 70798798 95101761 1587315512078371 14588864 58222558 70798800 95101767 158731552 2078373 1458886658222560 70798802 95101769 158731553 2169989 14588868 58222562 7079880495101777 158731554 2169990 14588870 58222564 70798806 98956195 1587315552172285 14588872 58222566 70798808 98956209 158731556 2173403 1459709858222568 70798810 98956219 158731557 2175768 14597112 58222570 7079881298956223 158731558 2175852 14597124 58222572 70798814 98956232 1587315592175867 14597127 58222575 70798816 98956244 158731560 2218123 1462574358222577 70798818 98956249 158731561 2239113 14625918 58222579 7079882098956255 158731562 2239115 14626493 58222581 70798824 98956261 1587315632253439 14716957 58222583 70798826 98956263 158731564 2266632 1471696158222585 70798828 98956271 158731565 2266634 14716969 58222587 7079883098956277 158731566 2291087 14716971 58222589 70798832 98956279 1587315672293965 14716973 58222591 70798834 98956281 158731568 2293967 1501145758222593 70798836 98956285 158731569 2306827 15099974 58222595 7079883898956289 158744132 2306829 15277619 58222597 70798840 98956291 1587441402345025 15419020 58222599 70798842 98956293 158744148 2345029 1585922058222601 70798844 98956299 158744156 2345031 15986229 58222603 7079884698956301 158744164 2345033 16508167 58222605 70798848 98956303 1587463552385484 16554974 58222607 70798850 98956305 158746363 2385486 1692318658222609 70798852 98956307 158746371

APPENDIX B GI Numbers of Lambda Light Chains Used to Derive the VλLibraries

31454 3142529 4566076 9968397 51103608 77379760 32808 3142531 45660789968401 51103612 77379824 32812 3142533 4566082 9968403 5110361477379826 33335 3142535 4566084 9968405 51103616 77379828 33368 31425374566086 9968409 51490956 77379830 33383 3142539 4566088 9968411 5478126177379832 33387 3142541 4566090 9968413 61815560 77379834 33412 31425434566092 9968415 62720404 77379836 33429 3142545 4566094 9968417 6272040677379838 33431 3142547 4566096 9968419 62720408 77379840 33433 31425494566098 9968421 62720412 77379842 33703 3142553 4566101 9968423 6286094777379846 33711 3142556 4566105 9968425 62860950 77379848 37918 31425584732059 9968427 62860967 77379850 37920 3142562 4761253 9968429 6286096977379855 37922 3142564 4761255 9968433 62860971 77379857 37923 31425664761257 9968435 62860973 77379859 38359 3142569 4761259 9968437 6286097577379861 38360 3142573 4761261 9968439 62860977 77379863 38364 31425774761263 10636511 62860979 77379865 38365 3142579 4761265 1063651462860985 77379867 38366 3142581 4761267 10636518 62861006 77379869 383683142583 4761269 10636521 62861008 77379871 186078 3142585 476127110636527 62861010 77379875 186080 3142587 4761273 11992185 6286104777379877 186082 3142589 4761277 11992187 62999489 77379879 1860843142591 4761279 11992189 62999497 77379882 186086 3142593 492795711992191 62999501 77379884 186088 3142595 5019504 11992195 6299950977379886 186090 3142597 5019506 11992197 70888031 77379888 1860923142599 5019516 11992199 70888035 77379890 186094 3142601 501951811992201 70888037 77379894 186096 3142603 5019520 12666922 7088804177379896 186097 3142612 5019528 12666924 70888043 77379900 1861113142614 5019530 12666926 70888045 77379908 186162 3142616 501953212666928 70888047 77379910 186164 3142618 5019534 12666930 7088804977379912 186168 3142620 5019536 12666932 70888051 77379916 1861703142649 5174362 12666934 70888053 77379918 186172 3142651 517436412666936 70888055 80975584 186175 3142653 5174366 12666938 7088805780975588 298556 3142656 5174378 12666940 70888059 80975598 4052233142658 5524086 12666942 70888061 80975622 405227 3142660 552410612666944 70888063 80975628 409040 3142662 5524108 12666946 7088806580975632 409041 3142668 5524118 12666948 70888067 80975636 4090433142670 5524122 12666952 70888069 81020028 433485 3142672 552413212666954 70888071 81020064 434041 3142674 5578817 12666956 7088807386438995 434045 3142676 5578819 12666958 70888075 86439001 4395143142678 5578823 12666960 70888077 86439005 439516 3142680 557882512666962 70888079 86439015 441251 3142684 5578827 12830380 7088808186439017 460854 3153359 5578829 12830382 70888083 86439087 4608563153361 5578831 12830384 70888085 86439089 460860 3153365 557883313276707 70888087 86439091 465157 3153366 5911837 13877276 7088808986439093 465167 3153368 6492194 14279402 70888091 86439095 4651713153374 6492196 14279404 70888093 86439097 465175 3153376 649220614279406 70888095 86439099 469249 3335577 6492208 17226627 7088809786439101 483911 3335579 6492210 17226649 70888099 86439105 4878243335585 6492212 18307305 70888103 86439127 487825 3335587 664307818307307 70888105 86439133 487828 3335591 6643082 18307309 7088810986439137 493153 3388046 6643086 18307311 70888111 86439139 5064263388048 6643088 18307313 70888113 86439141 506428 3388050 664309018307315 70888115 90994749 515765 3388054 6643098 18307317 7088811795007506 532599 3388056 6643104 18307319 70888121 95007546 5326003388058 6643106 18307321 70888123 95007548 532603 3388060 664311418307329 70888125 95007550 560845 3388062 6643118 21311290 7088812795007552 575230 3388064 6643120 21311292 70888129 95007554 5752383388066 6643124 21669150 70888133 95007556 575242 3388070 664312621669152 70888137 95007558 685021 3388072 6643128 21669154 7088813995007560 773591 3388074 6643136 21669156 70888141 95007562 8713623388080 6643138 21669158 70888143 95007564 987068 3747019 664315421669160 70888147 95007566 987076 3821077 6643156 21669162 7088814995007570 998390 3821078 6643158 21669164 70888151 95007572 9983943821079 6643162 21669166 70888155 95007576 1055278 3821080 664316821669172 70888157 95007578 1070329 3821081 6643170 21669174 70888159109240683 1070341 3821082 6643172 21669176 70888161 109240697 10703493821083 6643176 21669178 70888163 109240743 1143195 3821084 664317821669180 70888165 109240749 1200068 3821086 6643180 21669182 70888167109240754 1235776 3821087 6643182 21669184 70888169 109240756 12357783821089 6643184 21669186 70888171 109240758 1235780 3821090 664318621669188 70888173 116795127 1235782 3821091 6643188 21669190 70888179116795192 1255606 3821092 6643192 21669192 70888181 146336934 12556103821093 6643196 21669194 70888183 156632919 1255611 3821094 664319821669196 70888185 156632943 1255613 3821095 6643200 21669198 70888187156632945 1552313 3821096 6643202 21669200 70888193 156632975 15615993821097 6643204 21669204 70888195 156633095 1770407 4103646 664321021669206 70888197 156633103 1864134 4103648 6643214 21669210 70888199156633141 1864140 4103650 6643218 21669212 70888201 156633153 18641424103652 6643220 21669214 70888204 156633155 1864144 4103654 664322421669218 70888206 156633159 2078365 4103656 6643226 21669220 70888208156633171 2654039 4103658 6643230 21669222 70888210 156633179 26540434103660 6643232 21669224 70888212 156633199 2865485 4103672 664323821669226 70888216 156633203 3023094 4324023 6643240 21669228 70888218156633209 3023096 4324025 6643242 21669230 70888220 156633211 30230984324029 6643244 21669232 70888222 156633225 3023100 4324031 664324821669234 70888224 156633229 3023102 4324037 6643250 21669236 70888228156633237 3023104 4324039 6643254 21669238 70888230 156633241 30231064324043 6643256 21669240 70888232 156633245 3023108 4324047 664325821669242 70888234 156633253 3023110 4324055 6643268 21669244 70888236156633255 3023112 4324057 6643272 21669248 70888238 156633267 30231144324061 6643274 21669252 70888240 156633283 3023116 4324063 664327621669254 70888242 157093725 3023118 4324067 6643278 21669256 70888244170684323 3023120 4324069 6643280 21669260 70888246 170684325 30231224324073 6643282 21669262 70888248 170684329 3023126 4324075 664328621669264 70888250 170684331 3023130 4324077 6643290 21669266 70888252170684333 3023132 4324085 6643292 21669268 70888254 170684335 30911534324087 6643294 21669270 70888258 170684339 3091155 4324089 664329621669272 70888260 170684341 3091157 4324091 6643302 21669274 70888262170684345 3091159 4324093 6643304 21669276 70888264 170684349 30911614324097 6643308 21669278 70888266 170684351 3091163 4324103 664331421669280 70888268 170684355 3091165 4324107 6643318 21669288 70888270170684363 3091167 4324111 6643328 21998780 70888272 170684365 30911694324113 6643344 21998782 70888274 170684369 3091171 4324115 664335221998784 70888276 170684371 3091173 4324117 6643354 21998786 70888278170684373 3091175 4324123 6643358 21998792 70888280 170684375 30911774324125 6643360 21998794 70888282 170684379 3091179 4324127 664336221998800 70888284 170684381 3091181 4324139 6643366 21998802 70888286170684385 3091183 4324145 6643368 21998804 70888288 170684387 30911854324151 6643374 23194484 70888290 170684389 3091187 4324155 664337623194488 70888292 170684397 3091191 4324157 6643378 23194492 70888294170684405 3091193 4324159 6643382 23194496 70888296 170684407 30911954324163 6643386 23343556 70888304 170684409 3091197 4324169 664339024474079 70888306 170684411 3091201 4324175 6643392 27369031 71482628170684417 3091203 4324177 6643402 27369033 71482632 170684419 30912054324181 6643416 27369035 77378177 170684423 3091207 4324187 664341827369037 77378188 170684425 3091209 4324189 6643424 27369045 77378257170684427 3091213 4324193 6643428 27369047 77378266 170684429 30938614324197 6643436 27369051 77378268 170684431 3093863 4324199 664344627369053 77378270 170684433 3093865 4324205 6643448 27369058 77378273170684439 3093867 4324207 6643450 27369060 77378277 170684443 30938694324209 6643452 27369064 77378280 170684449 3093871 4324211 664345627369068 77378282 170684451 3093873 4324213 6643470 27369075 77378284170684453 3093875 4324215 6643474 27369082 77378286 170684461 30938774324221 6643478 27369084 77378288 170684469 3093879 4324223 664348427369088 77378291 170684473 3093881 4324229 6643488 27818828 77378293170684489 3093883 4324231 6643492 28394695 77378298 170684495 30938854324245 6643500 28394699 77378300 170684497 3093887 4324247 664351228394703 77378303 170684499 3093889 4324249 6643514 28394707 77378305170684501 3093891 4324251 6643528 28394711 77378307 170684507 30938954324255 6643534 28394715 77378309 170684513 3093903 4324257 664355828848877 77378312 170684515 3142451 4324261 6643560 28848881 77378316170684517 3142453 4324263 6643562 28848885 77378318 170684527 31424554324265 6643564 29342115 77378320 170684531 3142457 4324271 664357233304654 77378322 170684535 3142459 4324273 6643574 40647151 77378377170684537 3142461 4324275 6643580 47271301 77378379 170684539 31424654324283 6643582 47271303 77378381 170684541 3142467 4324285 664358447271319 77378383 170684545 3142471 4468355 6643586 47271321 77378385170684549 3142475 4468367 6643588 47271323 77378387 170684553 31424774468369 6643592 47271325 77378389 170684555 3142479 4468371 664359650199320 77378392 170684557 3142481 4565964 6643598 50199322 77378394170684561 3142483 4565966 6643600 50199328 77378396 170684565 31424854565996 6643602 50199330 77378398 170684567 3142487 4566007 664360450199338 77378400 170684569 3142489 4566009 6643606 50199340 77378402170684571 3142491 4566016 6643614 50871689 77379590 170684583 31424934566021 6643628 51103426 77379620 170684589 3142495 4566023 664363051103428 77379622 170684591 3142497 4566025 6649891 51103430 77379624170684593 3142499 4566029 6649893 51103434 77379632 170684597 31425034566045 8920222 51103436 77379642 170684599 3142505 4566049 892022651103572 77379644 170684601 3142507 4566051 9864840 51103574 77379646170684603 3142509 4566053 9968383 51103576 77379675 170684607 31425114566055 9968385 51103588 77379677 170684609 3142515 4566057 996838751103590 77379726 170684613 3142517 4566059 9968389 51103592 77379728170684617 3142519 4566061 9968391 51103600 77379730 170684619 31425214566065 9968393 51103602 77379738 3142527 4566074 9968395 5110360677379740

1-31. (canceled)
 32. A library of synthetic polynucleotides, whereinsaid polynucleotides encode a plurality of antibody VKCDR3 amino acidsequences comprising about 1 to about 10 of the amino acids found atKabat positions 89, 90, 91, 92, 93, 94, 95, 95A, 96, and 97, in selectedVKCDR3 amino acid sequences derived from a particular IGKV or IGKJgermline sequence.
 33. The library of claim 32, wherein the syntheticpolynucleotides encode one or more of the amino acid sequences listed inTable 33 or a sequence at least about 80% identical to any of them. 34.An antibody isolated from the polypeptide expression products of thelibrary of claim
 32. 35. A library of synthetic polynucleotides, whereinsaid polynucleotides encode a plurality of unique antibody VKCDR3 aminoacid sequences that are of at least about 80% identity to an amino acidsequence represented by the following formula:[VK_Chassis]-[L3-VK]-[X]-[JK*], wherein: (i) VK_Chassis is an amino acidsequence selected from the group consisting of about Kabat amino acid 1to about Kabat amino acid 88 encoded by IGKV1-05, IGKV1-06, IGKV1-08,IGKV1-09, IGKV1-12, IGKV1-13, IGKV1-16, IGKV1-17, IGKV1-27, IGKV1-33,IGKV1-37, IGKV1-39, IGKV1D-16, IGKV1D-17, IGKV1D-43, IGKV1D-8, IGKV2-24,IGKV2-28, IGKV2-29, IGKV2-30, IGKV2-40, IGKV2D-26, IGKV2D-29, IGKV2D-30,IGKV3-11, IGKV3-15, IGKV3-20, IGKV3D-07, IGKV3D-11, IGKV3D-20, IGKV4-1,IGKV5-2, IGKV6-21, IGKV6D-41, and a sequence of at least about 80%identity to any of them; (ii) L3-VK is the portion of the VKCDR3 encodedby the IGKV gene segment; and (iii) X is any amino acid residue; and(iv) JK* is an amino acid sequence selected from the group consisting ofamino acid sequences encoded by IGJK1, IGJK2, IGJK3, IGJK4, and IGJK5,wherein the first amino acid residue of each amino acid sequence is notpresent.
 36. An antibody isolated from the polypeptide expressionproducts of the library of claim
 35. 37. The library of claim 35,wherein X is selected from the group consisting of F, L, I, R, W, Y, andP.
 38. A library of synthetic polynucleotides, wherein saidpolynucleotides encode a plurality of VλCDR3 amino acid sequences thatare of at least about 80% identity to an amino acid sequence representedby the following formula:[Vλ_Chassis]-[L3-Vλ]-[Jλ], wherein: (i) Vλ_Chassis is an amino acidsequence selected from the group consisting of about Kabat amino acid 1to about Kabat amino acid 88 encoded by IGλV1-36, IGλV1-40, IGλV1-44,IGλV1-47, IGλV1-51, IGλV10-54, IGλV2-11, IGλV2-14, IGλV2-18, IGλV2-23,IGλV2-8, IGλV3-1, IGλV3-10, IGλV3-12, IGλV3-16, IGλV3-19, IGλV3-21,IGλV3-25, IGλV3-27, IGλV3-9, IGλV4-3, IGλV4-60, IGλV4-69, IGλV5-39,IGλV5-45, IGλV6-57, IGλV7-43, IGλV7-46, IGλV8-61, IGλV9-49, IGλV10-54,and a sequence of at least about 80% identity to any of them; (ii) L3-Vλis the portion of the VλCDR3 encoded by the IGλV segment; and (iii) Jλis an amino acid sequence selected from the group consisting of aminoacid sequences encoded by IGλJ1-01, IGXλJ2-01, IGλJ3-01, IGλJ3-02,IGλJ6-01, IGλJ7-01, and IGλJ7-02, and wherein the first amino acidresidue of each sequence may or may not be deleted.
 39. An antibodyisolated from the polypeptide expression products of the library ofclaim
 38. 40. A library of synthetic polynucleotides, wherein saidpolynucleotides encode a plurality of antibody proteins comprising: (i)at least 10⁶ unique antibody CDRH3 amino acid sequences comprising: (A)an N1 amino acid sequence of 0 to about 3 amino acids, wherein eachamino acid of the N1 amino acid sequence is among the 12 most frequentlyoccurring amino acids at the corresponding position in N1 amino acidsequences of CDRH3 amino acid sequences that are functionally expressedby human B cells; (B) a human CDRH3 DH amino acid sequence, N- andC-terminal truncations thereof, or a sequence of at least about 80%identity to any of them; (C) an N2 amino acid sequence of 0 to about 3amino acids, wherein each amino acid of the N2 amino acid sequence isamong the 12 most frequently occurring amino acids at the correspondingposition in N2 amino acid sequences of CDRH3 amino acid sequences thatare functionally expressed by human B cells; and (D) a human CDRH3 H3-JHamino acid sequence, N-terminal truncations thereof, or a sequence of atleast about 80% identity to any of them; and (ii) a VKCDR3 amino acidsequence comprising about 1 to about 10 of the amino acids found atKabat positions 89, 90, 91, 92, 93, 94, 95, 95A, 96, and 97, in selectedVKCDR3 amino acid sequences derived from a particular IGKV or IGKJgermline sequence.
 41. The library of claim 40, wherein the VKCDR3 aminoacid sequence comprises one or more of the amino acid sequences listedin Table 33 or a sequence at least about 80% identical to any of them.42. An antibody isolated from the library of claim
 40. 43. The libraryof claim 40, wherein the antibody proteins are expressed in aheterodimeric form.
 44. The library of claim 40, wherein the antibodyproteins are expressed as antibody fragments.
 45. The library of claim44, wherein the antibody fragments are selected from the groupconsisting of Fab, Fab′, F(ab′)2, Fv fragments, diabodies, linearantibodies, and single-chain antibodies.
 46. A library of syntheticpolynucleotides, wherein said polynucleotides encode a plurality ofantibody proteins comprising: (i) at least 106 unique antibody CDRH3amino acid sequences comprising: (a) an N1 amino acid sequence of 0 toabout 3 amino acids, wherein each amino acid of the N1 amino acidsequence is among the 12 most frequently occurring amino acids at thecorresponding position in N1 amino acid sequences of CDRH3 amino acidsequences that are functionally expressed by human B cells; (b) a humanCDRH3 DH amino acid sequence, N- and C-terminal truncations thereof, ora sequence of at least about 80% identity to any of them; (c) an N2amino acid sequence of 0 to about 3 amino acids, wherein each amino acidof the N2 amino acid sequence is among the 12 most frequently occurringamino acids at the corresponding position in N2 amino acid sequences ofCDRH3 amino acid sequences that are functionally expressed by human Bcells; and (d) a human CDRH3 H3-JH amino acid sequence, N-terminaltruncations thereof, or a sequence of at least about 80% identity to anyof them; and (ii) a VKCDR3 amino acid sequence of at least about 80%identity to a amino acid sequence represented by the following formula:[VK_Chassis]-[L3-VK]-[X]-[JK*], wherein: (a) VK_Chassis is an amino acidsequence selected from the group consisting of about Kabat amino acid 1to about Kabat amino acid 88 encoded by IGKV1-05, IGKV1-06, IGKV1-08,IGKV1-09, IGKV1-12, IGKV1-13, IGKV1-16, IGKV1-17, IGKV1-27, IGKV1-33,IGKV1-37, IGKV1-39, IGKV1D-16, IGKV1D-17, IGKV1D-43, IGKV1D-8, IGKV2-24,IGKV2-28, IGKV2-29, IGKV2-30, IGKV2-40, IGKV2D-26, IGKV2D-29, IGKV2D-30,IGKV3-11, IGKV3-15, IGKV3-20, IGKV3D-07, IGKV3D-11, IGKV3D-20, IGKV4-1,IGKV5-2, IGKV6-21, and IGKV6D-41, or a sequence of at least about 80%identity to any of them; (b) L3-VK is the portion of the VKCDR3 encodedby the IGKV gene segment; and (c) X is any amino acid residue; and (d)JK* is an amino acid sequence selected from the group consisting ofamino acid sequences encoded by IGJK1, IGJK2, IGJK3, IGJK4, and IGJK5,wherein the first residue of each IGJK amino acid sequence is notpresent.
 47. An antibody isolated from the library of claim
 46. 48-72.(canceled)
 73. The library according to any one of claims 32, 35, 40,and 46, wherein the synthetic polynucleotides encode at least 102 of theVKCDR3 amino acid sequences encoded by the polynucleotides of SEQ IDNOs: 259-379, or sequences at least about 80% identical said VKCDR3polypeptides.
 74. The library according to any one of claims 40 and 46wherein the antibody proteins are expressed in heterodimeric form. 75.The library according to claim 74, wherein the antibody proteins areexpressed as full length antibodies, Fab fragments, Fab′ fragments,F(ab′)2 fragments, diabodies, linear antibodies, or single chainantibodies.
 76. A method of preparing a synthetic polynucleotide librarycomprising providing and assembling the polynucleotide sequencesaccording to any one of claims 32, 35, 38, 40, and
 46. 77. The method ofclaim 76, wherein the method comprises split-pool synthesis.
 78. Themethod of claim 76, further comprising providing a 5′ polynucleotidesequence and a 3′ polynucleotide sequence, wherein said 5′ sequence and3′ sequence facilitate homologous recombination.
 79. The method of claim76, wherein the method further comprises: recombining the assembledCDRH3 encoding polynucleotide sequences with an acceptor vectorcomprising heavy chain chassis sequences; recombining the assembledVKCDR3 encoding polynucleotide sequences with an acceptor vectorcomprising light chain chassis sequences; or recombining the assembledVλCDR3 encoding polynucleotide sequences with an acceptor vectorcomprising light chain chassis sequences.
 80. The method according toany one of claims 77, 78, and 79, wherein the recombining is performedin yeast.
 81. The method of claim 80, wherein the yeast is S.cerevisiae.